2PFX
Crystal structure of uncharacterized peroxidase-related protein (YP_614459.1) from Silicibacter sp. TM1040 at 1.70 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.5 | 277 | NANODROP, 0.1M NaCl, 30.0% PEG 200, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.069 | α = 90 |
b = 85.069 | β = 90 |
c = 105.616 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 MIRROR (VERTICAL FOCUSING) | 2007-02-01 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837, 0.97908, 0.97929 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.7 | 27.842 | 100 | 0.113 | 0.113 | 5.4 | 5.6 | 47633 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.74 | 100 | 0.437 | 0.437 | 1.7 | 5.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MAD | FREE R | 1.7 | 27.84 | 49885 | 2281 | 100 | 0.117 | 0.114 | 0.165 | RANDOM EXPANDED BY TWIN LAW | 19.798 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
2887 | 3307.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_similar_dist | 0.065 |
s_zero_chiral_vol | 0.05 |
s_non_zero_chiral_vol | 0.049 |
s_angle_d | 0.027 |
s_from_restr_planes | 0.026 |
s_similar_adp_cmpnt | 0.026 |
s_anti_bump_dis_restr | 0.024 |
s_bond_d | 0.008 |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2977 |
Nucleic Acid Atoms | |
Solvent Atoms | 315 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
MolProbity | model building |
SHELX | phasing |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
SHELXD | phasing |
SOLVE | phasing |
SHELXL-97 | refinement |