3KJJ
Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (hexagonal crystal form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 294 | VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 155.613 | α = 90 |
b = 155.613 | β = 90 |
c = 116.189 | 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 225 mm CCD | 2005-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97950 | 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 | 1.9 | 30 | 100 | 0.154 | 31.2 | 27.4 | 126653 | -1.5 | 19.6 |
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 | 1.9 | 1.97 | 99.9 | 0.758 | 3.2 | 15.5 | 12608 |
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 | 1.9 | 29.88 | 120095 | 6478 | 99.07 | 0.1678 | 0.16574 | 0.20629 | RANDOM | 24.636 |
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] | |
-14.07 | -14.07 | 28.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.857 |
r_dihedral_angle_4_deg | 18.133 |
r_dihedral_angle_3_deg | 15.644 |
r_dihedral_angle_1_deg | 5.6 |
r_scangle_it | 5.257 |
r_scbond_it | 4.018 |
r_mcangle_it | 2.751 |
r_mcbond_it | 1.769 |
r_angle_refined_deg | 1.077 |
r_chiral_restr | 0.071 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10893 |
Nucleic Acid Atoms | |
Solvent Atoms | 801 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
SOLVE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |