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Crystal structure of human UBA5 in complex with UFM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WXS 1WXS and 3H8V experimental model PDB 3H8V 1WXS and 3H8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 8% Tascimate, pH 7.0 and 16% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.32 62.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.081 α = 90 b = 138.081 β = 90 c = 99.178 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS 6M 2015-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.896 BESSY 14.3
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 1.85 76.3 100 0.174 11.6 18.5 93040
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85
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 1WXS and 3H8V 1.85 69.04 88360 4641 99.99 0.18834 0.18741 0.1908 0.20605 0.2061 RANDOM 42.487
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] 29.33 29.33 -58.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.967 r_dihedral_angle_4_deg 15.428 r_dihedral_angle_3_deg 13.925 r_long_range_B_refined 6.737 r_long_range_B_other 6.733 r_dihedral_angle_1_deg 6.489 r_scangle_other 3.366 r_scbond_it 2.513 r_scbond_other 2.513 r_mcangle_it 2.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.967 r_dihedral_angle_4_deg 15.428 r_dihedral_angle_3_deg 13.925 r_long_range_B_refined 6.737 r_long_range_B_other 6.733 r_dihedral_angle_1_deg 6.489 r_scangle_other 3.366 r_scbond_it 2.513 r_scbond_other 2.513 r_mcangle_it 2.407 r_mcangle_other 2.407 r_angle_refined_deg 1.766 r_mcbond_it 1.599 r_mcbond_other 1.599 r_angle_other_deg 1.393 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5070 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing