2V3Z
Glu383Ala Escherichia coli aminopeptidase P in complex with substrate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WL9 | PDB ENTRY 1WL9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 277 | CRYSTALLISED IN 30% PEG 4K, 0.1 M TRIS PH 8.8 AT 277K. SOAKED IN 30% PEG 4K, 0.1 M TRIS PH 8.5, 1 MM MNCL2, 5 MM VAL-PRO-LEU, 10% MPD FOR 30 MIN AT 277K IMMEDIATELY PRIOR TO DATA COLLECTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.4 | 72.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 177.695 | α = 90 |
b = 177.695 | β = 90 |
c = 96.433 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 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 | 100 | CCD | ADSC CCD | MIRRORS | 2006-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | APS | 23-ID-B |
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 | 1.56 | 50 | 99.4 | 0.07 | 32.5 | 11 | 125677 | -3 | 17.78 |
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 | 1.56 | 1.62 | 99.8 | 0.58 | 4.3 | 10 |
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 1WL9 | 1.56 | 29.66 | 121838 | 3825 | 99.4 | 0.14 | 0.14 | 0.15 | RANDOM | 10.84 |
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] | |
0.11 | 0.05 | 0.11 | -0.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.315 |
r_dihedral_angle_4_deg | 16.367 |
r_dihedral_angle_3_deg | 11.156 |
r_dihedral_angle_1_deg | 5.832 |
r_scangle_it | 5.7 |
r_scbond_it | 3.923 |
r_mcangle_it | 2.396 |
r_mcbond_it | 2.206 |
r_angle_refined_deg | 1.348 |
r_angle_other_deg | 0.902 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3519 |
Nucleic Acid Atoms | |
Solvent Atoms | 731 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | phasing |