2YQB
Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4AWW | PDB ENTRY 4AWW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 20MM MES PH 6.5, 20% PEG3350, 0.2M SODIUM CITRATE, 200 MM NACL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 127.849 | α = 90 |
b = 127.849 | β = 90 |
c = 86.628 | 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 | PIXEL | DECTRIS PILATUS 6M | MIRRORS | 2012-10-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | Diamond | I24 |
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 | 1.41 | 18.08 | 99.9 | 0.09 | 9.5 | 4.6 | 102529 | 9.7 |
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 | 1.41 | 1.48 | 100 | 0.59 | 2.3 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4AWW | 1.41 | 18.07 | 97401 | 5122 | 100 | 0.11342 | 0.11163 | 0.14693 | RANDOM | 8.983 |
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] | |
-0.09 | -0.04 | -0.09 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.923 |
r_dihedral_angle_4_deg | 19.776 |
r_dihedral_angle_3_deg | 12.143 |
r_dihedral_angle_1_deg | 6.669 |
r_scangle_it | 5.069 |
r_scbond_it | 3.563 |
r_mcangle_it | 2.29 |
r_angle_refined_deg | 1.607 |
r_mcbond_it | 1.573 |
r_rigid_bond_restr | 1.452 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3421 |
Nucleic Acid Atoms | |
Solvent Atoms | 809 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |