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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000032a
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 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.028 α = 90 b = 56.998 β = 90 c = 115.098 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 1.42 57.54 100 0.059 0.064 0.025 0.999 12.4 6.3 65414
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 1.42 1.46 100 1.5 1.664 0.711 0.512 5.4 4799
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5aho 1.42 57.54 61823 3134 99.29 0.1771 0.1754 0.2108 0.2041 RANDOM 24.73
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] -0.02 0.61 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.336 r_sphericity_free 32.751 r_sphericity_bonded 12.894 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_4_deg 10.462 r_dihedral_angle_1_deg 6.033 r_mcangle_it 2.716 r_mcbond_it 2.066 r_mcbond_other 2.062 r_angle_refined_deg 1.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.336 r_sphericity_free 32.751 r_sphericity_bonded 12.894 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_4_deg 10.462 r_dihedral_angle_1_deg 6.033 r_mcangle_it 2.716 r_mcbond_it 2.066 r_mcbond_other 2.062 r_angle_refined_deg 1.359 r_rigid_bond_restr 1.248 r_angle_other_deg 0.943 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 308 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing