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PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with NM450-1
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 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.68 α = 90 b = 59.68 β = 90 c = 214.53 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 2017-07-07 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 1.78 51.68 100 0.128 0.135 0.043 0.999 12.4 9.6 43715
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 1.78 1.83 100 2.356 2.48 0.769 0.635 10.2 3147
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 1.78 51.74 41450 2185 99.89 0.2089 0.207 0.2362 0.2451 0.2741 RANDOM 35.519
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 34.284 r_dihedral_angle_4_deg 20.631 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_1_deg 9.958 r_mcangle_it 4.48 r_mcbond_it 2.501 r_mcbond_other 2.501 r_angle_refined_deg 1.509 r_angle_other_deg 1.252 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 20.631 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_1_deg 9.958 r_mcangle_it 4.48 r_mcbond_it 2.501 r_mcbond_other 2.501 r_angle_refined_deg 1.509 r_angle_other_deg 1.252 r_chiral_restr 0.075 r_bond_refined_d 0.01 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 3115 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing