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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 274)
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% PEG 1000, 0.1M MIB buffer
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.764 α = 90 b = 56.876 β = 90 c = 114.753 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 2017-04-12 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 1.43 56.87 100 0.048 0.052 0.021 0.999 13.8 6.3 63420
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 1.43 1.47 99.8 1.322 1.462 0.615 0.543 5.5 4629
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 1.43 56.87 60020 3043 99.34 0.1954 0.1939 0.2038 0.2245 0.2349 RANDOM 28.713
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] -0.1 0.93 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.905 r_dihedral_angle_4_deg 20.443 r_dihedral_angle_3_deg 12.786 r_dihedral_angle_1_deg 6.632 r_mcangle_it 5.005 r_mcbond_it 3.322 r_mcbond_other 3.313 r_angle_refined_deg 2.085 r_angle_other_deg 1.11 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.905 r_dihedral_angle_4_deg 20.443 r_dihedral_angle_3_deg 12.786 r_dihedral_angle_1_deg 6.632 r_mcangle_it 5.005 r_mcbond_it 3.322 r_mcbond_other 3.313 r_angle_refined_deg 2.085 r_angle_other_deg 1.11 r_chiral_restr 0.132 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.003 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 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing