3RGP
Structural and Kinetic Analysis of the Beef liver Catalase complexed with Nitric Oxide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4BLC | PDB entry code 4BLC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 298 | 1. 45-60mM Mg Formate mixed with 12-13 mg/ml protein containing 1-5 wt% of NH4OH. 2. Crystals then soaked overnight in 80 mM Mg-Formate solution, pH 6.7, 3. Finally soaked in 80 mM Mg formate and 150 mM bis-tris & 10-100mM DEANO, pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.02 | 59.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.11 | α = 90 |
b = 139.94 | β = 90 |
c = 228.02 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 315 | Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator | 2009-07-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.9 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.88 | 40.301 | 100 | 0.091 | 0.091 | 11.5 | 5.1 | 205859 | 205959 | 16.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.88 | 1.92 | 89.9 | 0.329 | 0.091 | 2.1 | 5.1 | 64188 |
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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry code 4BLC | 1.88 | 40.3 | 205859 | 205859 | 10125 | 92 | 0.18 | 0.18 | 0.18 | 0.214 | RANDOM | 22.8 |
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] | |
-3.43 | -2.87 | 6.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.2 |
c_scangle_it | 2.69 |
c_mcangle_it | 2.37 |
c_scbond_it | 1.93 |
c_mcbond_it | 1.75 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.96 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16068 |
Nucleic Acid Atoms | |
Solvent Atoms | 2020 |
Heterogen Atoms | 180 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |