1KP0
The Crystal Structure Analysis of Creatine Amidinohydrolase from Actinobacillus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CHM | PDB Entry 1CHM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 298 | PEG 6000, Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.26 | 62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 111.263 | α = 90 |
b = 113.624 | β = 90 |
c = 191.649 | γ = 90 |
Symmetry | |
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Space Group | I 2 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 | 293 | CCD | ADSC QUANTUM 4 | 2001-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-18B | 1.00 | Photon Factory | BL-18B |
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 | 2.7 | 40 | 99.8 | 0.065 | 10.6 | 33916 | 33902 | 2 | 2 | 27.6 |
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) | |||||||||||
2.7 | 2.85 | 99.9 | 0.151 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | PDB Entry 1CHM | 2.7 | 30 | 33576 | 33576 | 1672 | 99.6 | 0.191 | 0.191 | 0.188 | 0.222 | Random | 18.2 |
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] | |
2.67 | 3.18 | -0.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.5 |
c_scangle_it | 2.68 |
c_scbond_it | 1.8 |
c_mcangle_it | 1.54 |
c_angle_deg | 1.3 |
c_mcbond_it | 0.95 |
c_improper_angle_d | 0.82 |
c_bond_d | 0.007 |
o_bond_d_na | |
o_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6468 |
Nucleic Acid Atoms | |
Solvent Atoms | 118 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
CNS | refinement |
DPS | data reduction |
MOSFLM | data reduction |