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Vitamin D3 receptor/lithochoric acid derivative complex
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 0.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.78 30.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.045 α = 90 b = 36.898 β = 96.963 c = 39.486 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 95 PIXEL DECTRIS PILATUS 6M 2015-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 40 97.4 0.094 0.996 7.1 3.3 15052
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.13 0.63 0.91 1.63
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ZLC 2 40 15036 762 97.339 0.201 0.1977 0.1978 0.2678 0.2683 44.663
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] -5.813 -0.931 3.688 2.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.53 r_dihedral_angle_3_deg 16.167 r_dihedral_angle_4_deg 14.415 r_lrange_it 8.286 r_lrange_other 8.284 r_scangle_it 6.577 r_scangle_other 6.575 r_dihedral_angle_1_deg 6.291 r_mcangle_it 5.054 r_mcangle_other 5.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.53 r_dihedral_angle_3_deg 16.167 r_dihedral_angle_4_deg 14.415 r_lrange_it 8.286 r_lrange_other 8.284 r_scangle_it 6.577 r_scangle_other 6.575 r_dihedral_angle_1_deg 6.291 r_mcangle_it 5.054 r_mcangle_other 5.052 r_scbond_it 4.439 r_scbond_other 4.436 r_mcbond_it 3.543 r_mcbond_other 3.542 r_angle_refined_deg 1.578 r_angle_other_deg 1.333 r_nbd_other 0.246 r_nbd_refined 0.212 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.162 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1959 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing