☰ Navigation Tabs
Crystal structure of CYP2R1 in complex with vitamin D2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C6G PDB entry 3C6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 1.2M Ammonium sulfate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.85 68.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.361 α = 90 b = 163.393 β = 90 c = 152.289 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 2008-04-12 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 2.3 50 97.5 0.099 12.3 6.8 73584
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) 2.3 2.34 84.7 0.636 4.8 3156
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 3C6G 2.3 30 73363 2215 96.673 0.206 0.205 0.2163 0.231 0.2454 thin shells 37.917
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] 3.72 -2.344 -1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 22.598 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_1_deg 5.381 r_mcangle_it 2.337 r_scangle_it 1.817 r_mcbond_it 1.458 r_angle_refined_deg 1.273 r_scbond_it 1.228 r_angle_other_deg 1.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 22.598 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_1_deg 5.381 r_mcangle_it 2.337 r_scangle_it 1.817 r_mcbond_it 1.458 r_angle_refined_deg 1.273 r_scbond_it 1.228 r_angle_other_deg 1.056 r_mcbond_other 0.277 r_symmetry_vdw_other 0.255 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.196 r_nbd_other 0.184 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.144 r_nbtor_other 0.088 r_chiral_restr 0.086 r_bond_refined_d 0.015 r_symmetry_hbond_refined 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7444 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 405
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