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PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1929757385
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SY1 6SY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 293 0.1M Hepes, 0.1M Magnesium chloride, 20% PEG 6K, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.42 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.149 α = 90 b = 146.911 β = 102.9 c = 87.327 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-02-21 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9126 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.989 85.122 92.4 0.188 0.097 0.99 6.9 3.7 78185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.989 2.242 66.3 0.912 0.477 0.555 3.6
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 6SY1 1.98 85.12 74266 3950 58.32 0.1688 0.1657 0.1723 0.2248 0.2229 RANDOM 24.78
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] -0.23 0.19 -0.01 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_4_deg 15.808 r_dihedral_angle_3_deg 14.943 r_dihedral_angle_1_deg 7.556 r_mcangle_it 3.261 r_mcbond_it 2.018 r_mcbond_other 2.017 r_angle_refined_deg 1.529 r_angle_other_deg 1.296 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_4_deg 15.808 r_dihedral_angle_3_deg 14.943 r_dihedral_angle_1_deg 7.556 r_mcangle_it 3.261 r_mcbond_it 2.018 r_mcbond_other 2.017 r_angle_refined_deg 1.529 r_angle_other_deg 1.296 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13480 Nucleic Acid Atoms Solvent Atoms 1809 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing