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PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with EN08775-43
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 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.06 α = 90 b = 59.06 β = 90 c = 212.7 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 2018-02-16 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 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 1.92 49.73 98.8 0.189 0.2 0.067 0.995 10.3 9.2 33630
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 1.92 1.97 95.2 7.38 7.857 2.648 0.395 8.8 2375
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3BAP 1.92 49.78 31864 1684 98.74 0.2162 0.2136 0.2655 0.2539 RANDOM 31.716
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] 0.62 0.31 0.62 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 18.643 r_dihedral_angle_3_deg 15.431 r_dihedral_angle_1_deg 7.978 r_mcangle_it 4.53 r_mcbond_it 2.826 r_mcbond_other 2.822 r_angle_refined_deg 1.538 r_angle_other_deg 1.257 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.977 r_dihedral_angle_4_deg 18.643 r_dihedral_angle_3_deg 15.431 r_dihedral_angle_1_deg 7.978 r_mcangle_it 4.53 r_mcbond_it 2.826 r_mcbond_other 2.822 r_angle_refined_deg 1.538 r_angle_other_deg 1.257 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 254 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing