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OSH4 bound to an electrophilic oxysterol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZHY PDB ENTRY 1ZHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 12-14 % of PEG 20,000 in 50mM MES (pH 6.5) buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.62 α = 99.17 b = 65.689 β = 100.17 c = 77.939 γ = 96.76
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 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 1.7 20 95.8 0.038 14.1 1.9 103310
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) 1 1.7 1.73 94.6 0.159 1.9
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 PDB ENTRY 1ZHY 1.7 19.86 96113 5045 93.39 0.18229 0.18057 0.1893 0.21473 0.221 RANDOM 24.374
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] 0.51 0.33 0.33 -1.49 0.49 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.812 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_4_deg 13.046 r_dihedral_angle_1_deg 6.439 r_scbond_it 3.446 r_mcangle_it 3.178 r_mcbond_it 2.26 r_mcbond_other 2.26 r_angle_refined_deg 2.009 r_angle_other_deg 0.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.812 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_4_deg 13.046 r_dihedral_angle_1_deg 6.439 r_scbond_it 3.446 r_mcangle_it 3.178 r_mcbond_it 2.26 r_mcbond_other 2.26 r_angle_refined_deg 2.009 r_angle_other_deg 0.995 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6884 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 68
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BOS data collection MOLREP phasing