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PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event map: SETDB1 in complex with FMOMB000017a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DLM 3DLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 25% PEG-3350, 0.2M lithium sulfate, 0.1M Bis-tris
Crystal Properties Matthews coefficient Solvent content 2.4 48.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.79 α = 90 b = 64.05 β = 90 c = 70.81 γ = 90
Symmetry Space Group P 21 21 21
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 2015-10-11 M 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 1.58 43.82 99.9 0.073 0.079 0.031 0.999 14.4 6.5 35453
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 1.58 1.62 99.9 1.497 1.622 0.62 0.555 6.7 2573
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 3DLM 1.58 43.86 33585 1814 99.83 0.1944 0.193 0.2154 0.2197 0.2401 RANDOM 23.455
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] 0.18 -0.54 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.945 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 11.739 r_dihedral_angle_1_deg 6.775 r_mcangle_it 2.987 r_mcbond_other 1.871 r_mcbond_it 1.869 r_angle_refined_deg 1.631 r_angle_other_deg 1.359 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.945 r_dihedral_angle_4_deg 19.88 r_dihedral_angle_3_deg 11.739 r_dihedral_angle_1_deg 6.775 r_mcangle_it 2.987 r_mcbond_other 1.871 r_mcbond_it 1.869 r_angle_refined_deg 1.631 r_angle_other_deg 1.359 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing