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Crystal structure of Uba4-Urm1 from Chaetomium thermophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YUB D_1292108208
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES pH 7.5 and 20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.49 72.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.735 α = 90 b = 197.735 β = 90 c = 99.566 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2019-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.15 42.87 99.78 0.06226 0.066 0.02106 1 18.85 9.9 13003 166.81
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 3.15 3.263 5.447 4.72 1.91 0.297
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 D_1292108208 3.15 42.87 10082 503 77.62 0.2131 0.2103 0.2279 0.2631 0.2767 RANDOM 142.709
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] 1.01 0.5 1.01 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.577 r_dihedral_angle_1_deg 21.522 r_dihedral_angle_3_deg 21.301 r_dihedral_angle_4_deg 20.482 r_angle_refined_deg 1.525 r_angle_other_deg 1.13 r_chiral_restr 0.021 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_refined
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.577 r_dihedral_angle_1_deg 21.522 r_dihedral_angle_3_deg 21.301 r_dihedral_angle_4_deg 20.482 r_angle_refined_deg 1.525 r_angle_other_deg 1.13 r_chiral_restr 0.021 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_refined r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2879 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing