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PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with SK-430
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 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.01 α = 90 b = 59.01 β = 90 c = 212.964 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 1.68 70.99 100 0.077 0.081 0.026 0.999 13.2 9.6 49996
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 1.68 1.78 100 2.822 3.007 1.026 0.486 8.5 7167
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 1.68 70.99 46727 2436 98.45 0.2157 0.2133 0.2276 0.2592 0.265 RANDOM 40.004
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] 0.7 0.35 0.7 -2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.667 r_dihedral_angle_4_deg 19.478 r_dihedral_angle_3_deg 14.374 r_dihedral_angle_1_deg 7.349 r_mcangle_it 5.167 r_mcbond_other 3.377 r_mcbond_it 3.368 r_angle_refined_deg 1.628 r_angle_other_deg 1.278 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.667 r_dihedral_angle_4_deg 19.478 r_dihedral_angle_3_deg 14.374 r_dihedral_angle_1_deg 7.349 r_mcangle_it 5.167 r_mcbond_other 3.377 r_mcbond_it 3.368 r_angle_refined_deg 1.628 r_angle_other_deg 1.278 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 247 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing