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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 281)
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 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.61 α = 90 b = 57.12 β = 90 c = 115 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 1.77 57.12 100 0.068 0.074 0.029 0.999 14.3 6.4 33955
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 1.77 1.82 100 1.645 1.796 0.716 0.464 6.2 2466
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 1.77 57.12 32218 1677 99.89 0.1981 0.1956 0.2047 0.2448 0.2523 RANDOM 40.605
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] 0.39 -0.81 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 19.083 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.201 r_mcangle_it 5.345 r_mcbond_it 3.643 r_mcbond_other 3.639 r_angle_refined_deg 1.772 r_angle_other_deg 1.058 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 19.083 r_dihedral_angle_3_deg 13.121 r_dihedral_angle_1_deg 6.201 r_mcangle_it 5.345 r_mcbond_it 3.643 r_mcbond_other 3.639 r_angle_refined_deg 1.772 r_angle_other_deg 1.058 r_chiral_restr 0.118 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