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Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NLL TR Half-Complex from PDB Entry 2NLL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.06 59.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.5 α = 90 b = 61.5 β = 90 c = 241.97 γ = 90
Symmetry Space Group P 43 21 2
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 APS-1 2001-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.0332 APS 19-BM
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 2.8 50 99.5 0.1 27.2 14.1 12384 -3 79.8
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) 2.8 2.9 99 0.39 2.3 1173
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 TR Half-Complex from PDB Entry 2NLL 2.8 50 11200 11200 1124 91.6 0.214 0.2122 0.272 0.2713 RANDOM 76
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] 24.32 24.32 -48.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 2.53 c_mcangle_it 1.91 c_angle_deg 1.7 c_scbond_it 1.54 c_improper_angle_d 1.31 c_mcbond_it 1.08 c_bond_d 0.015 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 2.53 c_mcangle_it 1.91 c_angle_deg 1.7 c_scbond_it 1.54 c_improper_angle_d 1.31 c_mcbond_it 1.08 c_bond_d 0.015 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 1468 Nucleic Acid Atoms 732 Solvent Atoms 31 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing