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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 FMOPL000010a
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 2.09 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.38 α = 90 b = 74.09 β = 96.19 c = 63.08 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 1.61 33.6 99.1 0.096 0.115 0.062 0.996 8.1 3.3 43891
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 1.61 1.65 99.9 1.08 1.285 0.69 0.528 3.4 3240
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 1.61 62.71 41738 2130 98.98 0.1733 0.1715 0.1841 0.2088 0.2198 RANDOM 25.093
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] 2.2 0.15 -1.37 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_dihedral_angle_4_deg 20.206 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_1_deg 6.602 r_mcangle_it 2.961 r_mcbond_it 2.042 r_mcbond_other 2.041 r_angle_refined_deg 1.933 r_angle_other_deg 1.088 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_dihedral_angle_4_deg 20.206 r_dihedral_angle_3_deg 13.967 r_dihedral_angle_1_deg 6.602 r_mcangle_it 2.961 r_mcbond_it 2.042 r_mcbond_other 2.041 r_angle_refined_deg 1.933 r_angle_other_deg 1.088 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 274 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing