1VJR
Crystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 6.5 | 273 | 2M sodium chloride, 0.1M MES pH 6.5, 0.1M sodium dihydrogen phosphate, 0.1M potassium dihydrogen phosphate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.35 | 76.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.998 | α = 90 |
b = 93.998 | β = 90 |
c = 160.365 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | 2003-05-22 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.9797, 0.9999, 0.9799 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.4 | 94 | 100 | 0.072 | 14.5 | 4.6 | 28916 | 57.98 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.4 | 2.46 | 100 | 0.537 | 2.3 | 4.8 | 2087 |
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 | MAD | THROUGHOUT | 2.4 | 51.17 | 27354 | 1485 | 99.92 | 0.1653 | 0.16381 | 0.19427 | RANDOM | 44.646 |
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] | |
1.56 | 1.56 | -3.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.945 |
r_dihedral_angle_3_deg | 14.025 |
r_dihedral_angle_4_deg | 13.771 |
r_scangle_it | 8.85 |
r_scbond_it | 6.486 |
r_dihedral_angle_1_deg | 5.828 |
r_mcangle_it | 3.092 |
r_mcbond_it | 2.08 |
r_angle_refined_deg | 1.427 |
r_nbd_refined | 0.198 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2030 |
Nucleic Acid Atoms | |
Solvent Atoms | 279 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |
autoSHARP | phasing |
REFMAC | refinement |
CCP4 | data scaling |