☰ Navigation Tabs
Crystal structure of the kelch domain of human KLHL7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VPJ PDB entry 2VPJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 12% PEG 20000, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.435 α = 90 b = 50.905 β = 113.19 c = 87.5 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 IV 2009-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54180
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 1.63 28.34 99.2 0.083 13.8 6.5 38411 38407 2 17.4
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 1.63 1.72 98.8 0.636 2.6 6 5515
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2VPJ 1.63 28.34 2 38407 36483 1924 99.16 0.16284 0.1614 0.16138 0.18996 0.196 RANDOM 8.797
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] -0.21 0.13 -0.07 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.736 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 11.081 r_scangle_it 6.94 r_dihedral_angle_1_deg 6.934 r_scbond_it 5.377 r_mcangle_it 3.472 r_mcbond_it 2.174 r_angle_refined_deg 1.336 r_angle_other_deg 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.736 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 11.081 r_scangle_it 6.94 r_dihedral_angle_1_deg 6.934 r_scbond_it 5.377 r_mcangle_it 3.472 r_mcbond_it 2.174 r_angle_refined_deg 1.336 r_angle_other_deg 0.838 r_mcbond_other 0.542 r_chiral_restr 0.093 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2240 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 100
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling