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PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with FMOPL000464a
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 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.85 α = 90 b = 59.85 β = 90 c = 215.19 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 1.84 71.73 99.2 0.085 0.09 0.03 0.999 16.8 9.3 39681
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 1.84 1.89 100 1.921 2.034 0.662 0.583 9.3 2906
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 1.84 71.73 37646 1956 99.01 0.2109 0.2082 0.2219 0.2598 0.2716 RANDOM 36.143
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] 0.45 0.23 0.45 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.354 r_dihedral_angle_4_deg 21.057 r_dihedral_angle_3_deg 15.019 r_dihedral_angle_1_deg 8.096 r_mcangle_it 5.23 r_mcbond_it 3.72 r_mcbond_other 3.699 r_angle_refined_deg 1.8 r_angle_other_deg 1.289 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.354 r_dihedral_angle_4_deg 21.057 r_dihedral_angle_3_deg 15.019 r_dihedral_angle_1_deg 8.096 r_mcangle_it 5.23 r_mcbond_it 3.72 r_mcbond_other 3.699 r_angle_refined_deg 1.8 r_angle_other_deg 1.289 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3160 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing