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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000728a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AHO 5aho
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 30% PEG1000, 0.1 M MIB buffer
Crystal Properties Matthews coefficient Solvent content 2.2 44.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.123 α = 90 b = 57.114 β = 90 c = 115.21 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 PIXEL DECTRIS PILATUS 6M 2017-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 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 1.18 57.12 97.4 0.05 0.054 0.022 0.999 11.5 5.4 110721
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 1.18 1.21 76.6 0.9 1.098 0.609 0.589 2.9 6392
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 5aho 1.18 57.12 104783 5397 96.89 0.1787 0.1774 0.1781 0.2045 0.205 RANDOM 21.798
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] 0.16 0.31 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_sphericity_free 31.875 r_dihedral_angle_4_deg 13.475 r_sphericity_bonded 13.02 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.594 r_mcangle_it 2.637 r_mcbond_it 2.019 r_mcbond_other 2.007 r_rigid_bond_restr 1.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.442 r_sphericity_free 31.875 r_dihedral_angle_4_deg 13.475 r_sphericity_bonded 13.02 r_dihedral_angle_3_deg 12.083 r_dihedral_angle_1_deg 6.594 r_mcangle_it 2.637 r_mcbond_it 2.019 r_mcbond_other 2.007 r_rigid_bond_restr 1.502 r_angle_refined_deg 1.473 r_angle_other_deg 1.003 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2692 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing