3ML0
Thermostable Penicillin G acylase from Alcaligenes faecalis in tetragonal form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GK9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 303 | 15% PEG 8000, 0.1M Tris-Hcl pH7.5, 100uL b-octyl-glucopyranoside (0.50% w/v), vapor diffusion, hanging drop, temperature 303K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.22 | 61.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.558 | α = 90 |
b = 85.558 | β = 90 |
c = 298.804 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 295 | IMAGE PLATE | RIGAKU RAXIS IV++ | Mirrors | 2006-04-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.514 |
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 | 3.5 | 82.2 | 90.8 | 0.099 | 7.42 | 2.25 | 14860 | 1 | 29.99 |
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 | 3.499 | 3.59 | 89.67 | 0.239 | 3.08 | 2.01 | 13376 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1GK9 | 3.5 | 20 | 1 | 14860 | 13376 | 680 | 90.03 | 0.313 | 0.269 | 0.269 | 0.283 | RANDOM | 47.781 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.93 | 3.93 | -7.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.804 |
r_dihedral_angle_3_deg | 15.267 |
r_dihedral_angle_4_deg | 9.4 |
r_dihedral_angle_1_deg | 3.086 |
r_angle_refined_deg | 0.724 |
r_mcangle_it | 0.134 |
r_scangle_it | 0.084 |
r_mcbond_it | 0.075 |
r_chiral_restr | 0.047 |
r_scbond_it | 0.047 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5995 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |