5F2H
2.75 Angstrom resolution crystal structure of uncharacterized protein from Bacillus cereus ATCC 10987
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 295 | Protein (SeMet): 8.9 mg/ml in 10 mM Tris-HCl pH 8.3 0.25 M NaCl, 5 mM BME Crystallization: The Classics II D7(43): 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350 Cryo: Crystallization condition soak |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.25 | 45.3 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 71.067 | α = 90 |
b = 42.176 | β = 92.45 |
c = 106.032 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2014-10-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.75 | 30 | 100 | 0.097 | 31 | 7.4 | 16616 | 69.7 |
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 | 2.75 | 2.8 | 100 | 0.634 | 3.3 | 7.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.75 | 27.17 | 15767 | 836 | 99.4 | 0.23319 | 0.23019 | 0.29052 | RANDOM | 83.11 |
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] | |
10.46 | -2.32 | 2.73 | -13.05 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 19.412 |
r_dihedral_angle_4_deg | 9.129 |
r_dihedral_angle_3_deg | 7.281 |
r_angle_refined_deg | 1.511 |
r_dihedral_angle_1_deg | 1.267 |
r_angle_other_deg | 0.92 |
r_chiral_restr | 0.102 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5027 |
Nucleic Acid Atoms | |
Solvent Atoms | 20 |
Heterogen Atoms | 24 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
BLU-MAX | data collection |
HKL-3000 | data scaling |
HKL-3000 | phasing |
Coot | model building |
ARP | model building |
HKL-3000 | data reduction |