1YJL
Reduced Peptidylglycine alpha-Hydroxylating Monooxygenase 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 = 59.764 | α = 90 |
b = 66.019 | β = 90 |
c = 69.526 | 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 4 | MIRRORS | 2004-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.1 | NSLS | X25 |
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 | 2.4 | 65.94 | 99.5 | 0.065 | 0.065 | 4.3 | 4.5 | 11174 | 11174 | -3.7 | 51.3 |
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) | ||||||||||
2.4 | 2.53 | 99.68 | 0.445 | 0.445 | 1.7 | 4.6 | 1577 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1OPM | 2.4 | 47.67 | 11141 | 11141 | 535 | 99.28 | 0.209 | 0.209 | 0.206 | 0.274 | RANDOM | 50.951 |
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] | |
0.64 | 1.68 | -2.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.942 |
r_dihedral_angle_4_deg | 20.314 |
r_dihedral_angle_3_deg | 19.179 |
r_dihedral_angle_1_deg | 8.824 |
r_scangle_it | 3.496 |
r_scbond_it | 2.344 |
r_angle_refined_deg | 1.927 |
r_mcangle_it | 1.765 |
r_mcbond_it | 1.053 |
r_nbtor_refined | 0.318 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2245 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms |
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 |