3MW8
Crystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255) from SHEWANELLA AMAZONENSIS SB2B at 1.65 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1500M di-ammonium hydrogen phosphate, 33.0000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.39 | α = 90 |
b = 50.073 | β = 90.04 |
c = 58.255 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2010-03-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 |
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 | 1.65 | 38.525 | 99.2 | 0.048 | 13.48 | 35551 | -3 | 25.002 |
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) | |||||||||||
1.65 | 1.71 | 99.8 | 0.442 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.65 | 38.525 | 35537 | 1814 | 99.26 | 0.177 | 0.175 | 0.203 | RANDOM | 29.321 |
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] | |
0.26 | -1.48 | -0.86 | 0.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.784 |
r_dihedral_angle_4_deg | 22.58 |
r_dihedral_angle_3_deg | 13.025 |
r_scangle_it | 7.541 |
r_dihedral_angle_1_deg | 6.002 |
r_scbond_it | 5.099 |
r_mcangle_it | 3.063 |
r_mcbond_it | 2.013 |
r_angle_refined_deg | 1.576 |
r_angle_other_deg | 0.977 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1770 |
Nucleic Acid Atoms | |
Solvent Atoms | 226 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
SHELX | phasing |
MolProbity | model building |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |