4A8P
Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N5-(phosphonoacetyl)-L-ornithine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4A8H | PDB ENTRY 4A8H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 0.2 M AMMONIUM ACETATE, 25% POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS PH 5.5, 1 MM N5- (PHOSPHONOACETYL)-L-ORNITHINE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.52 | α = 105.43 |
b = 81.71 | β = 102.8 |
c = 82.28 | γ = 100.75 |
Symmetry | |
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Space Group | P 1 |
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 | MARRESEARCH | 2009-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 30 | 87.5 | 0.12 | 10.9 | 1.6 | 114553 | 2 | 27.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 30 | 87.5 | 0.42 | 1.8 | 1.6 |
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 4A8H | 2 | 25 | 108160 | 5763 | 87.57 | 0.198 | 0.19593 | 0.23732 | RANDOM | 33.299 |
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] | |
-0.59 | -1.12 | -0.94 | -0.41 | -1.11 | -0.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.733 |
r_dihedral_angle_4_deg | 16.611 |
r_dihedral_angle_3_deg | 12.363 |
r_dihedral_angle_1_deg | 4.762 |
r_scangle_it | 1.321 |
r_angle_refined_deg | 1.009 |
r_scbond_it | 0.833 |
r_mcangle_it | 0.423 |
r_mcbond_it | 0.223 |
r_chiral_restr | 0.07 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15479 |
Nucleic Acid Atoms | |
Solvent Atoms | 535 |
Heterogen Atoms | 114 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |