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SdcA in complex with the E2, UbcH5C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 1.5 M ammonium sulfate, 3% glycerol, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.72 66.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.55 α = 90 b = 142.203 β = 90 c = 118.338 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 210 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.6309 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 50 96.4 8.8 4 25193
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 2.9 2.95
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 4TRG 3.01 50 21100 1140 96.27 0.19746 0.19406 0.2034 0.26053 0.2714 RANDOM 80.161
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] 4.45 -1.75 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.096 r_dihedral_angle_3_deg 17.428 r_dihedral_angle_4_deg 14.786 r_long_range_B_refined 9.225 r_long_range_B_other 9.225 r_dihedral_angle_1_deg 6.652 r_scangle_other 6.284 r_mcangle_it 6.125 r_mcangle_other 6.125 r_scbond_it 3.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.096 r_dihedral_angle_3_deg 17.428 r_dihedral_angle_4_deg 14.786 r_long_range_B_refined 9.225 r_long_range_B_other 9.225 r_dihedral_angle_1_deg 6.652 r_scangle_other 6.284 r_mcangle_it 6.125 r_mcangle_other 6.125 r_scbond_it 3.801 r_scbond_other 3.8 r_mcbond_it 3.778 r_mcbond_other 3.777 r_angle_refined_deg 1.468 r_angle_other_deg 0.804 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5350 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing