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PanDDA analysis group deposition -- Crystal Structure of DCLRE1A in complex with FMOPL000676a
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 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.892 α = 90 b = 57.04 β = 90 c = 115.019 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 1.35 57.02 100 0.051 0.055 0.022 1 12.4 6.1 75755
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 1.35 1.39 99.7 1.396 1.567 0.701 0.515 4.9 5517
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 1.35 57.02 71078 3648 98.58 0.1764 0.1746 0.1757 0.211 0.2115 RANDOM 25.772
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] 0.28 0.84 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.452 r_sphericity_free 33.204 r_sphericity_bonded 13.635 r_dihedral_angle_4_deg 12.83 r_dihedral_angle_3_deg 11.604 r_dihedral_angle_1_deg 6.126 r_mcangle_it 2.735 r_mcbond_it 2.059 r_mcbond_other 2.042 r_angle_refined_deg 1.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.452 r_sphericity_free 33.204 r_sphericity_bonded 13.635 r_dihedral_angle_4_deg 12.83 r_dihedral_angle_3_deg 11.604 r_dihedral_angle_1_deg 6.126 r_mcangle_it 2.735 r_mcbond_it 2.059 r_mcbond_other 2.042 r_angle_refined_deg 1.342 r_rigid_bond_restr 1.223 r_angle_other_deg 0.946 r_chiral_restr 0.08 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 311 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing