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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 66)
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 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.707 α = 90 b = 57.026 β = 90 c = 115.005 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 2016-09-29 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 1.68 28.75 98.4 0.05 0.054 0.021 1 22.8 6.6 39048
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 1.68 1.72 95.4 0.855 0.929 0.359 0.778 6.5 2749
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 1.68 28.75 37115 1900 98.06 0.1775 0.1755 0.1875 0.2162 0.2264 RANDOM 32.438
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] -0.57 1.6 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.237 r_dihedral_angle_4_deg 16.795 r_dihedral_angle_3_deg 12.621 r_dihedral_angle_1_deg 6.51 r_mcangle_it 4.636 r_mcbond_it 3.161 r_mcbond_other 3.158 r_angle_refined_deg 1.845 r_angle_other_deg 1.064 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.237 r_dihedral_angle_4_deg 16.795 r_dihedral_angle_3_deg 12.621 r_dihedral_angle_1_deg 6.51 r_mcangle_it 4.636 r_mcbond_it 3.161 r_mcbond_other 3.158 r_angle_refined_deg 1.845 r_angle_other_deg 1.064 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