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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000532a
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 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.803 α = 90 b = 56.833 β = 90 c = 114.683 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 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 1.43 56.82 100 0.046 0.05 0.02 1 14.1 6.3 63364
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 1.43 1.47 100 1.373 1.521 0.647 0.56 5.4 4629
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 1.43 56.82 59904 3029 99.33 0.1619 0.1598 0.203 0.1998 RANDOM 28.142
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] -0.35 1.27 -0.92
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.804 r_dihedral_angle_2_deg 34.45 r_dihedral_angle_4_deg 15.937 r_sphericity_bonded 13.683 r_dihedral_angle_3_deg 11.308 r_dihedral_angle_1_deg 6.236 r_mcangle_it 3.484 r_mcbond_it 2.661 r_mcbond_other 2.635 r_rigid_bond_restr 1.568
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.804 r_dihedral_angle_2_deg 34.45 r_dihedral_angle_4_deg 15.937 r_sphericity_bonded 13.683 r_dihedral_angle_3_deg 11.308 r_dihedral_angle_1_deg 6.236 r_mcangle_it 3.484 r_mcbond_it 2.661 r_mcbond_other 2.635 r_rigid_bond_restr 1.568 r_angle_refined_deg 1.384 r_angle_other_deg 0.949 r_chiral_restr 0.087 r_bond_refined_d 0.012 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 309 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing