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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 FF000014a
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 7 293 27.3% Tacsimate pH 7.0, 0.15 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.774 α = 90 b = 50.774 β = 90 c = 154.078 γ = 90
Symmetry Space Group P 41 2 2
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 2017-08-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.97625 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 1.95 51.41 100 0.111 0.116 0.033 0.999 14 12.1 15563
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 1.95 2 100 1.169 1.223 0.356 0.509 11.6 1106
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 1.95 50.77 14351 810 97.44 0.2056 0.203 0.2119 0.2537 0.2593 RANDOM 34.551
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] 0.61 0.61 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.441 r_dihedral_angle_4_deg 16.124 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 6.874 r_mcangle_it 4.158 r_mcbond_it 2.964 r_mcbond_other 2.962 r_angle_refined_deg 1.828 r_angle_other_deg 0.993 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.441 r_dihedral_angle_4_deg 16.124 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 6.874 r_mcangle_it 4.158 r_mcbond_it 2.964 r_mcbond_other 2.962 r_angle_refined_deg 1.828 r_angle_other_deg 0.993 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1331 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing