X/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 1ARC | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION | 8 | 297 | 20% w/v PEG 3350, 10mM Tris, HCl pH 8.0, 50% PEG 3350, HCl pD 8.0, VAPOR DIFFUSION, temperature 297K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.1 | 41.31 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 39.574 | α = 64.82 |
b = 40.785 | β = 66.1 |
c = 43.98 | γ = 73.42 |
Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | neutron | 297 | IMAGE PLATE | | BIX-4, SILICON | 2007-06-12 | M | SINGLE WAVELENGTH |
2 | 1 | x-ray | 297 | IMAGE PLATE | MAC Science DIP-2000 | double mirror | 2007-05-01 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | NUCLEAR REACTOR | JRR-3M BEAMLINE 1G-C | 2.6 | JRR-3M | 1G-C |
2 | ROTATING ANODE | MACSCIENCE M06X | 1.5418 | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 1.98 | 50 | 89.4 | 0.161 | | | | | | 4.87 | | | 11000 | | | |
2 | 1.895 | 50 | 89.4 | 0.078 | | | | | | 17.38 | | | 16128 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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2 | 1.88 | 1.95 | | 0.198 | | | | | | 5.95 | | |
2 | 1.95 | 2.03 | | 0.17 | | | | | | 7.2 | | |
2 | 2.03 | 2.12 | | 0.135 | | | | | | 9.3 | | |
2 | 2.12 | 2.23 | | 0.121 | | | | | | 10.5 | | |
2 | 2.23 | 2.37 | | 0.112 | | | | | | 11.6 | | |
2 | 2.37 | 2.55 | | 0.099 | | | | | | 13 | | |
2 | 2.55 | 2.81 | | 0.086 | | | | | | 15.3 | | |
2 | 2.81 | 3.21 | | 0.075 | | | | | | 17.8 | | |
2 | 3.21 | 4.05 | | 0.062 | | | | | | 23 | | |
2 | 4.05 | 80 | | 0.062 | | | | | | 23.3 | | |
2 | 2 | 2.07 | | 0.319 | | | | | | 2.5 | | |
2 | 2.07 | 2.15 | | 0.342 | | | | | | 2.9 | | |
2 | 2.15 | 2.25 | | 0.33 | | | | | | 3.2 | | |
2 | 2.25 | 2.37 | | 0.329 | | | | | | 2.9 | | |
2 | 2.37 | 2.52 | | 0.288 | | | | | | 3.3 | | |
2 | 2.52 | 2.71 | | 0.289 | | | | | | 3.7 | | |
2 | 2.71 | 2.99 | | 0.247 | | | | | | 4.5 | | |
2 | 2.99 | 3.42 | | 0.18 | | | | | | 6.7 | | |
2 | 3.42 | 4.31 | | 0.139 | | | | | | 9.7 | | |
2 | 4.31 | 50 | | 0.124 | | | | | | 10.7 | | |
1 | 2 | 2.07 | | 0.319 | | | | | | 2.51 | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | | 1.895 | 20.358 | | 2.08 | | 16081 | 800 | 89.99 | | 0.1493 | 0.1466 | 0.2028 | | |
NEUTRON DIFFRACTION | | 1.979 | 37.61 | | | | 10998 | 554 | 69.97 | | 0.1984 | 0.1952 | 0.2595 | | |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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-2.3375 | 1.7676 | 2.5966 | 4.4118 | -2.9931 | -2.0743 |
-0.058 | -1.3327 | 0.8508 | -1.2985 | 0.8387 | -3.4569 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 16.315 |
f_angle_d | 1.473 |
f_chiral_restr | 0.096 |
f_bond_d | 0.011 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1920 |
Nucleic Acid Atoms | |
Solvent Atoms | 140 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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MacScience | data collection |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |