☰ Navigation Tabs
Crystal structure of human WD repeat domain 5 with compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.171 α = 90 b = 93.467 β = 107.24 c = 64.786 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 100 IMAGE PLATE RIGAKU RAXIS HTC VeriMax HR 2011-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.82 50 100 0.086 25 7.2 104206 104206 23.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.85 100 0.807 2.12 6.4 5202
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-Factor (All) 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 2O9K 1.82 50 104206 103163 1043 99.77 0.17757 0.17759 0.17729 0.1779 0.20612 0.2063 RANDOM 25.61
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] 2.2 1.52 -0.98 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_4_deg 23.264 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 6.844 r_scangle_it 1.567 r_angle_refined_deg 1.134 r_scbond_it 0.988 r_mcangle_it 0.645 r_mcbond_it 0.35 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_4_deg 23.264 r_dihedral_angle_3_deg 13.264 r_dihedral_angle_1_deg 6.844 r_scangle_it 1.567 r_angle_refined_deg 1.134 r_scbond_it 0.988 r_mcangle_it 0.645 r_mcbond_it 0.35 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9233 Nucleic Acid Atoms Solvent Atoms 822 Heterogen Atoms 228
Software Software Software Name Purpose StructureStudio data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling