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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000166a
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 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.22 α = 90 b = 57.126 β = 90 c = 115.159 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 1.57 28.79 99.9 0.045 0.049 0.019 1 22.5 6.6 48938
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 1.57 1.61 98.8 0.75 0.814 0.313 0.818 6.6 3537
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 1.57 28.79 46519 2352 99.82 0.1503 0.1481 0.1486 0.1924 0.193 RANDOM 29.511
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] 0.38 0.74 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.558 r_sphericity_free 33.165 r_sphericity_bonded 14.124 r_dihedral_angle_4_deg 14.064 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_1_deg 6.438 r_mcangle_it 3.425 r_mcbond_it 2.723 r_mcbond_other 2.7 r_rigid_bond_restr 1.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.558 r_sphericity_free 33.165 r_sphericity_bonded 14.124 r_dihedral_angle_4_deg 14.064 r_dihedral_angle_3_deg 12.294 r_dihedral_angle_1_deg 6.438 r_mcangle_it 3.425 r_mcbond_it 2.723 r_mcbond_other 2.7 r_rigid_bond_restr 1.734 r_angle_refined_deg 1.446 r_angle_other_deg 0.984 r_chiral_restr 0.092 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 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing