3KXA
Crystal Structure of NGO0477 from Neisseria gonorrhoeae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 294 | 0.1M Tris HCl, 22% PEG 400, 0.3M tri-sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.823 | α = 90 |
b = 124.823 | β = 90 |
c = 137.577 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 225 mm CCD | 2006-04-10 | M | MAD | ||||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 225 mm CCD | 2006-02-18 | M | MAD | ||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97800 | ESRF | BM14 |
2 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.90499 | ESRF | BM14 |
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 | 2.8 | 30 | 99.7 | 0.238 | 10.3 | 10.7 | 19515 | -1 | 48.9 |
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) | |||||||||||
1,2 | 2.8 | 2.9 | 97.3 | 0.923 | 2.2 | 8.5 | 1929 |
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 | 2.8 | 26.31 | 18502 | 1004 | 99.39 | 0.23236 | 0.2298 | 0.27968 | RANDOM | 42.253 |
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] | |
2.61 | 1.3 | 2.61 | -3.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.8 |
r_dihedral_angle_4_deg | 20.632 |
r_dihedral_angle_3_deg | 19.547 |
r_scangle_it | 14.634 |
r_scbond_it | 9.405 |
r_mcangle_it | 7.55 |
r_dihedral_angle_1_deg | 5.842 |
r_mcbond_it | 4.749 |
r_angle_refined_deg | 1.174 |
r_chiral_restr | 0.071 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4062 |
Nucleic Acid Atoms | |
Solvent Atoms | 27 |
Heterogen Atoms | 71 |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |