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Crystal structure of CYP2R1 in complex with vitamin D3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SUO PDB ENTRY 1SUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 1.1M Ammonium sulfate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.89 68.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.68 α = 90 b = 163.051 β = 90 c = 152.755 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment 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 2006-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall 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 2.7 30 98.5 0.138 9.1 7.1 47597
Highest Resolution Shell 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) 2.7 2.8 86.2 0.809 4.9 4116
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SUO 2.8 29.34 42392 2132 99.6 0.195 0.193 0.2033 0.231 0.237 RANDOM 34.036
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.4 -0.24 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.249 r_dihedral_angle_4_deg 22.467 r_dihedral_angle_3_deg 15.761 r_dihedral_angle_1_deg 5.295 r_mcangle_it 2.611 r_scangle_it 2.315 r_mcbond_it 2.141 r_scbond_it 1.605 r_angle_refined_deg 1.259 r_angle_other_deg 0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.249 r_dihedral_angle_4_deg 22.467 r_dihedral_angle_3_deg 15.761 r_dihedral_angle_1_deg 5.295 r_mcangle_it 2.611 r_scangle_it 2.315 r_mcbond_it 2.141 r_scbond_it 1.605 r_angle_refined_deg 1.259 r_angle_other_deg 0.849 r_mcbond_other 0.32 r_symmetry_vdw_other 0.249 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.206 r_nbd_other 0.186 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.083 r_chiral_restr 0.065 r_bond_refined_d 0.014 r_xyhbond_nbd_other 0.012 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7556 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 303
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection