1YIP
Oxidized Peptidylglycine Alpha-Hydroxylating Monooxygenase (PHM) in a New Crystal Form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1OPM | PDB ENTRY 1OPM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.523 | α = 90 |
b = 65.683 | β = 90 |
c = 69.871 | 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 | IMAGE PLATE | RIGAKU RAXIS IV | mirrors | 2004-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.54 |
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 | 2.2 | 30.01 | 92.9 | 0.058 | 0.058 | 12.04 | 4.7 | 14064 | 14064 | -3.7 | 38.84 |
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) | ||||||||||
2.2 | 2.32 | 100 | 0.444 | 0.444 | 2.18 | 4.7 | 2026 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1OPM | 2.2 | 30.01 | 2 | 14034 | 14034 | 687 | 98.908 | 0.192 | 0.192 | 0.1895 | 0.2389 | RANDOM | 38.582 |
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] | |
-2.59 | 2.739 | -0.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.563 |
r_dihedral_angle_4_deg | 17.949 |
r_dihedral_angle_3_deg | 17.266 |
r_dihedral_angle_1_deg | 8.542 |
r_scangle_it | 3.173 |
r_scbond_it | 2.205 |
r_angle_refined_deg | 1.822 |
r_mcangle_it | 1.383 |
r_scangle_other | 1.309 |
r_mcbond_it | 1.121 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2425 |
Nucleic Acid Atoms | |
Solvent Atoms | 158 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
CCP4 | data scaling |
AMoRE | phasing |