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Crystal structures of rat VDR-LBD with W282R mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 MOPS-Na, di-Ammonium Citrate, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.143 α = 90 b = 42.281 β = 95.53 c = 41.846 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2007-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 50 30677 23.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71
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 2ZLC 1.65 35.27 30677 3051 93.6 0.185 0.185 0.1846 0.229 0.2301 RANDOM 27.6
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] -7.76 -2.41 7.26 0.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.7 c_scangle_it 5.19 c_scbond_it 3.73 c_mcangle_it 2.28 c_angle_deg 1.7 c_mcbond_it 1.45 c_improper_angle_d 1.28 c_bond_d 0.019 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.7 c_scangle_it 5.19 c_scbond_it 3.73 c_mcangle_it 2.28 c_angle_deg 1.7 c_mcbond_it 1.45 c_improper_angle_d 1.28 c_bond_d 0.019 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1938 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing