☰ Navigation Tabs
Crystal structure of the Kelch domain of human KBTBD5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOZ PDB ENTRY 2WOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M CITRATE PH 5.3, 20%(W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.52 51.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.33 α = 90 b = 64.95 β = 90 c = 89.2 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2012-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.78 39.89 99.9 0.07 13.9 6.2 34642 2 18.12
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 1.78 1.82 99.9 0.56 3.1 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WOZ 1.78 52.51 32847 1744 99.75 0.18053 0.17815 0.22623 0.219 RANDOM 18.116
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] 0.79 -0.18 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.134 r_dihedral_angle_4_deg 21.679 r_dihedral_angle_3_deg 13.801 r_dihedral_angle_1_deg 6.924 r_scangle_it 6.307 r_mcangle_it 3.555 r_scbond_it 2.41 r_mcbond_it 2.293 r_angle_refined_deg 1.661 r_angle_other_deg 0.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.134 r_dihedral_angle_4_deg 21.679 r_dihedral_angle_3_deg 13.801 r_dihedral_angle_1_deg 6.924 r_scangle_it 6.307 r_mcangle_it 3.555 r_scbond_it 2.41 r_mcbond_it 2.293 r_angle_refined_deg 1.661 r_angle_other_deg 0.904 r_symmetry_vdw_refined 0.364 r_symmetry_vdw_other 0.295 r_nbd_refined 0.268 r_nbd_other 0.23 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.177 r_nbtor_other 0.126 r_chiral_restr 0.106 r_xyhbond_nbd_refined 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_mcbond_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing