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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 119)
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 2.2 44.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.111 α = 90 b = 57.194 β = 90 c = 115.047 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 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 1.65 57.16 100 0.132 0.144 0.056 0.997 7.4 6.4 42265
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 1.65 1.69 100 1.969 2.143 0.84 0.527 6.4 3072
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 1.65 57.16 39023 1988 96.98 0.2141 0.2121 0.2222 0.2518 0.263 RANDOM 28.988
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] -0.4 1.11 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.642 r_dihedral_angle_4_deg 19.938 r_dihedral_angle_3_deg 12.779 r_dihedral_angle_1_deg 6.608 r_mcangle_it 3.971 r_mcbond_it 2.744 r_mcbond_other 2.744 r_angle_refined_deg 1.811 r_angle_other_deg 1.07 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.642 r_dihedral_angle_4_deg 19.938 r_dihedral_angle_3_deg 12.779 r_dihedral_angle_1_deg 6.608 r_mcangle_it 3.971 r_mcbond_it 2.744 r_mcbond_other 2.744 r_angle_refined_deg 1.811 r_angle_other_deg 1.07 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing