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Crystal Structure of the SRAP Domain of Human HMCES Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F20 2F20, 2BDV, 2ICU, 1ZN6 experimental model PDB 2BDV 2F20, 2BDV, 2ICU, 1ZN6 experimental model PDB 2ICU 2F20, 2BDV, 2ICU, 1ZN6 experimental model PDB 1ZN6 2F20, 2BDV, 2ICU, 1ZN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M BTP, 2% Tacsimate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.44 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.102 α = 90 b = 44.745 β = 107.15 c = 82.901 γ = 90
Symmetry Space Group I 1 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 PILATUS3 6M 2016-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 48.37 97 0.045 0.999 15.9 3.8 43639
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 93.2 0.679 0.667 1.9 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2F20, 2BDV, 2ICU, 1ZN6 1.5 48.37 41504 2132 96.6 0.1831 0.1818 0.19 0.2093 0.2154 RANDOM 24.169
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] -0.76 0.93 -0.61 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.357 r_dihedral_angle_4_deg 15.039 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_1_deg 6.398 r_mcangle_it 2.47 r_mcbond_it 1.574 r_mcbond_other 1.572 r_angle_refined_deg 1.499 r_angle_other_deg 0.971 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.357 r_dihedral_angle_4_deg 15.039 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_1_deg 6.398 r_mcangle_it 2.47 r_mcbond_it 1.574 r_mcbond_other 1.572 r_angle_refined_deg 1.499 r_angle_other_deg 0.971 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1986 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing