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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000085a
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 2.21 44.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.15 α = 90 b = 57.23 β = 90 c = 115.08 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 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 57.23 98.6 0.061 0.066 0.025 0.998 14.7 6.5 64858
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 97.3 1.437 1.583 0.652 0.461 5.7 4689
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 1.42 57.23 61674 3123 98.42 0.1589 0.1571 0.1571 0.194 0.195 RANDOM 27.675
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] -0.27 1.29 -1.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.488 r_dihedral_angle_2_deg 35.317 r_dihedral_angle_4_deg 14.945 r_sphericity_bonded 13.755 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 6.163 r_mcangle_it 2.755 r_mcbond_it 2.111 r_mcbond_other 2.105 r_angle_refined_deg 1.314
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.488 r_dihedral_angle_2_deg 35.317 r_dihedral_angle_4_deg 14.945 r_sphericity_bonded 13.755 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 6.163 r_mcangle_it 2.755 r_mcbond_it 2.111 r_mcbond_other 2.105 r_angle_refined_deg 1.314 r_rigid_bond_restr 0.995 r_angle_other_deg 0.947 r_chiral_restr 0.078 r_bond_refined_d 0.01 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 2696 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing