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Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CZH PDB entry 3CZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 1.2M Ammounium sulfate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.87 68.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.303 α = 90 b = 163.04 β = 90 c = 152.588 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 315 2008-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-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 2.72 50 99.9 0.163 8 7.2 46055
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) 2.72 2.77 100 0.957 7.2 2276
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3CZH 2.721 30 45761 1369 99.213 0.184 0.183 0.1892 0.218 0.219 thin shells (sftools) 37.005
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] 3.837 -2.163 -1.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.272 r_dihedral_angle_4_deg 22.841 r_dihedral_angle_3_deg 14.219 r_dihedral_angle_1_deg 5.462 r_mcangle_it 2.171 r_scangle_it 1.555 r_angle_refined_deg 1.392 r_mcbond_it 1.331 r_scbond_it 1.035 r_angle_other_deg 1.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.272 r_dihedral_angle_4_deg 22.841 r_dihedral_angle_3_deg 14.219 r_dihedral_angle_1_deg 5.462 r_mcangle_it 2.171 r_scangle_it 1.555 r_angle_refined_deg 1.392 r_mcbond_it 1.331 r_scbond_it 1.035 r_angle_other_deg 1.019 r_symmetry_vdw_other 0.284 r_nbd_refined 0.211 r_mcbond_other 0.198 r_nbtor_refined 0.186 r_nbd_other 0.185 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.092 r_nbtor_other 0.088 r_symmetry_hbond_refined 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7453 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 386
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-3000 data reduction REFMAC phasing