1ML2
Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase with Zn(II)-(20-oxo-Protoporphyrin IX)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MK8 | PDB Entry : 1MK8 - H52Y1 Structure |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 2-Methyl-2,4-Pentanediol (MPD), tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.487 | α = 90 |
b = 50.998 | β = 90 |
c = 118.759 | 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 | 116 | IMAGE PLATE | RIGAKU RAXIS IV | 2001-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.54178 |
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 | 1.65 | 100 | 91.2 | 0.044 | 0.051 | 44.47 | 11.74 | 34532 | 2 | 2 |
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) | ||||||||||
1.65 | 1.68 | 86.8 | 0.127 | 0.121 | 11.36 | 4.67 | 1614 |
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-Work (Depositor) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry : 1MK8 - H52Y1 Structure | 1.65 | 50 | 37716 | 34380 | 1741 | 91.2 | 0.1831 | 0.2151 | RANDOM | 18.5538 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_d | 1.18 |
o_bond_d | 0.0048 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2384 |
Nucleic Acid Atoms | |
Solvent Atoms | 506 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
X-GEN | data reduction |
AMoRE | phasing |
CNS | refinement |
X-GEN | data scaling |