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PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with FMOPL000387a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BAP 3BAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 277 0.1M acetate pH 5.1, 0.0025M ZnAC, 6% PEG3K
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.63 α = 90 b = 59.63 β = 90 c = 215.04 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 2017-07-08 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 2.28 107.52 99.5 0.218 0.232 0.076 0.996 9.2 9.2 21066
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 2.28 2.34 95.1 9.819 10.471 3.571 0.506 8.6 1446
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 FOURIER SYNTHESIS THROUGHOUT 3BAP 2.28 71.78 19948 1054 99.29 0.2121 0.2085 0.2286 0.2786 0.2896 RANDOM 40.464
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] -0.21 -0.1 -0.21 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 19.328 r_dihedral_angle_3_deg 15.166 r_dihedral_angle_1_deg 8.068 r_mcangle_it 5.314 r_mcbond_other 3.47 r_mcbond_it 3.468 r_angle_refined_deg 1.615 r_angle_other_deg 1.208 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.598 r_dihedral_angle_4_deg 19.328 r_dihedral_angle_3_deg 15.166 r_dihedral_angle_1_deg 8.068 r_mcangle_it 5.314 r_mcbond_other 3.47 r_mcbond_it 3.468 r_angle_refined_deg 1.615 r_angle_other_deg 1.208 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3160 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing