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Crystal Structure of Ubiquitin-like Domain of Human WDR12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DTC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 2.5M NH4SO4, 0.1M NaOAc pH4.6
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.197 α = 90 b = 50.91 β = 94.11 c = 47.811 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN A200 2019-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.72 50 98.6 0.076 0.084 0.034 10.7 5.7 20767
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.75 78.4 0.438 0.518 0.269 0.816 3
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 5DTC 1.72 23.86 19675 1073 98.53 0.1767 0.1743 0.1862 0.2229 0.2329 RANDOM 14.779
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] 0.14 0.02 0.37 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 12.504 r_dihedral_angle_4_deg 8.381 r_dihedral_angle_1_deg 6.577 r_angle_refined_deg 1.358 r_angle_other_deg 1.353 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.333 r_dihedral_angle_3_deg 12.504 r_dihedral_angle_4_deg 8.381 r_dihedral_angle_1_deg 6.577 r_angle_refined_deg 1.358 r_angle_other_deg 1.353 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 20
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data processing