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PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with FMOPL000271a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LZK 5LZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.8M NaP monobasic, 0.8M KP dibasic, 0.1M HEPES pH 7.5 5%(w/v) PEG10K
Crystal Properties Matthews coefficient Solvent content 2.1 41.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.47 α = 90 b = 74.22 β = 96.29 c = 63.05 γ = 90
Symmetry Space Group P 1 21 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 2016-07-09 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 1.73 31.93 98.8 0.109 0.129 0.069 0.996 8.1 3.4 35382
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 1.73 1.77 98.4 0.996 1.202 0.664 0.46 3.2 2604
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 5LZK 1.73 62.67 33676 1686 98.54 0.1762 0.1739 0.1847 0.2219 0.2286 RANDOM 24.7
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] 1.89 0.08 -1.32 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_4_deg 17.35 r_dihedral_angle_3_deg 14.055 r_dihedral_angle_1_deg 6.835 r_mcangle_it 2.929 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.873 r_angle_other_deg 1.061 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.128 r_dihedral_angle_4_deg 17.35 r_dihedral_angle_3_deg 14.055 r_dihedral_angle_1_deg 6.835 r_mcangle_it 2.929 r_mcbond_it 1.987 r_mcbond_other 1.987 r_angle_refined_deg 1.873 r_angle_other_deg 1.061 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2745 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing