2XLU
Joint-functions of protein residues and NADP(H) in oxygen-activation by flavin-containing monooxygenase: complex with thioNADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VQ7 | PDB ENTRY 2VQ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 7.5 | 277 | CRYSTALS WERE OBTAINED USING MICROBATCH TECHNIQUE UNDER 100% PARAFFIN OIL AT 4 C BY MIXING EQUAL VOLUMES OF 8 MG PROTEIN/ML IN 25 MM TRIS/HCL PH 8.0, 250 MM NACL, 1 MM NADP (OR ANALOGUE), AND 20% (W/V) PEG4000 IN 100 MM NA/HEPES PH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.3 | 71.4 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 220.679 | ¦Á = 90 |
b = 220.679 | ¦Â = 90 |
c = 130.531 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 |
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 CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
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 | 2.6 | 42 | 99.9 | 0.12 | 9.7 | 5 | 110842 |
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 | 2.6 | 2.74 | 100 | 0.41 | 3.7 | 4.9 |
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 2VQ7 | 2.6 | 41.15 | 105293 | 5537 | 99.94 | 0.21204 | 0.20997 | 0.25188 | RANDOM | 28.502 |
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] | |
-1.57 | -0.78 | -1.57 | 2.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.223 |
r_dihedral_angle_3_deg | 17.817 |
r_dihedral_angle_4_deg | 14.904 |
r_dihedral_angle_1_deg | 7.244 |
r_scangle_it | 3.727 |
r_scbond_it | 2.312 |
r_angle_refined_deg | 2.009 |
r_mcangle_it | 1.456 |
r_mcbond_it | 0.742 |
r_chiral_restr | 0.136 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14620 |
Nucleic Acid Atoms | |
Solvent Atoms | 427 |
Heterogen Atoms | 440 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |