4C3U
Extensive counter-ion interactions with subtilisin in aqueous medium, Cs derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WUV | PDB ENTRY 2WUV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SUBTILISIN CARLSBERG WAS PURCHASED FROM SIGMA (PRODUCT CODE: P5380) AND USED FOR CRYSTALLIZATION WITHOUT FURTHER PURIFICATION. THE PROTEIN POWDER WAS DISSOLVED IN 330 MM NA CACODYLATE BUFFER AT PH 5.6 TO A CONCENTRATION OF 10 MG/ML. SUBTILISIN WAS CRYSTALLIZED BY THE BATCH METHOD FROM BUFFER SOLUTION SATURATED WITH NA2SO4 13% (W/V) AS PRECIPITANT1. LONG NEEDLE-LIKE CRYSTALS GREW OVER A PERIOD OF TWO WEEKS TO TYPICAL DIMENSIONS 50 X 50 X 400 UM X UM X UM |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.167 | α = 90 |
b = 55.226 | β = 90 |
c = 75.85 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2005-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | SRS | PX10.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | ||||||||
1 | 2.28 | 50 | 99.9 | 0.12 | 10.6 | 5.8 | 10346 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.28 | 2.36 | 99.2 | 0.21 | 6.9 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2WUV | 2.29 | 33.92 | 9812 | 497 | 99.78 | 0.16 | 0.15626 | 0.23431 | RANDOM | 31.361 |
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] | |
0.43 | -0.32 | -0.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.447 |
r_dihedral_angle_4_deg | 17.356 |
r_dihedral_angle_3_deg | 15.691 |
r_dihedral_angle_1_deg | 6.164 |
r_scbond_it | 2.912 |
r_mcangle_it | 2.908 |
r_mcbond_it | 2.028 |
r_angle_refined_deg | 1.718 |
r_chiral_restr | 0.117 |
r_bond_refined_d | 0.014 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1920 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |