3QH8
Crystal structure of a beta-lactamase-like protein bound to AMP from brucella melitensis, long wavelength synchrotron data
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3MD7 | PDB entry 3md7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 290 | 15-18% PEG 3350, 200MM K/NA TARTRATE, 100MM BISTRISPROPANE PH 8.0, BRABA.11339.A.PW27637 AT 18MG/ML SUPPLEMENTED WITH 1MM AMPPNP AND 2MM MGCL2 AT 18MG/ML. CRYO: 21% PEG 3350, 15% EG, 165MM K/NA TARTRATE, 87MM BISTRISPROPANE PH 8.0, 1MM AMPPNP, 2MM MGCL2, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.21 | α = 90 |
b = 75.53 | β = 90 |
c = 98.94 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 QUANTUM 315r | 2010-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.3476 | ALS | 5.0.2 |
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 | 1.6 | 20 | 99.6 | 0.069 | 25.08 | 12.3 | 36517 | 36362 | -3 | 20.91 |
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 | 1.6 | 1.64 | 95.9 | 0.39 | 5.8 | 6.1 | 36362 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | 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 | MR | THROUGHOUT | PDB entry 3md7 | 1.6 | 18.88 | 36362 | 36263 | 1868 | 99.4 | 0.145 | 0.145 | 0.143 | 0.166 | RANDOM | 10.64 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.2 | -0.2 | 0.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.757 |
r_dihedral_angle_4_deg | 16.3 |
r_dihedral_angle_3_deg | 10.998 |
r_dihedral_angle_1_deg | 6.181 |
r_scangle_it | 4.038 |
r_scbond_it | 2.549 |
r_mcangle_it | 1.657 |
r_angle_refined_deg | 1.652 |
r_angle_other_deg | 0.983 |
r_mcbond_it | 0.937 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2118 |
Nucleic Acid Atoms | |
Solvent Atoms | 314 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
BOS | data collection |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |