2QTZ
Crystal Structure of the NADP+-bound FAD-containing FNR-like Module of Human Methionine Synthase Reductase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 277 | 0.1M Tris HCl, 0.2M KBr, 15% PEG 4000, crystals soaked in saturating levels of NADP+, pH 7.5, vapor diffusion, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.784 | α = 90 |
b = 67.235 | β = 106.91 |
c = 78.615 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | monochromator | 2005-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 0.934 | ESRF | ID14-3 |
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 | 1.9 | 19.94 | 98.4 | 0.052 | 13 | 40436 | 40436 |
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 | 1.9 | 1.97 | 97.4 | 0.304 | 4002 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.9 | 19.94 | 40156 | 40156 | 2014 | 100 | 0.17663 | 0.17663 | 0.175 | 0.211 | RANDOM | 29.246 |
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] | |
-0.03 | -0.03 | -0.01 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.006 |
r_dihedral_angle_4_deg | 17.065 |
r_dihedral_angle_1_deg | 13.773 |
r_dihedral_angle_3_deg | 13.709 |
r_scangle_it | 3.806 |
r_scbond_it | 2.406 |
r_mcangle_it | 1.603 |
r_angle_refined_deg | 1.493 |
r_mcbond_it | 1.006 |
r_nbtor_refined | 0.309 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3494 |
Nucleic Acid Atoms | |
Solvent Atoms | 352 |
Heterogen Atoms | 74 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |