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PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z1699011516
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MP0 PDB entry 5MP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.1 M acetate, pH 4.5, 5-25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.28 α = 90 b = 60.35 β = 90 c = 65 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 2M 2017-07-26 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 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 1.65 37.7 98.9 0.046 0.05 0.02 0.999 18.2 6.4 23208
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 1.65 1.69 97.9 1.117 1.237 0.521 0.645 5.5 1654
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 PDB entry 5MP0 1.65 44.27 22035 1133 98.6 0.1969 0.1948 0.2223 0.2396 0.2509 RANDOM 33.456
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] 1.79 -1.97 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.08 r_dihedral_angle_4_deg 20.782 r_dihedral_angle_3_deg 16.033 r_dihedral_angle_1_deg 7.002 r_mcangle_it 4.635 r_mcbond_it 3.22 r_mcbond_other 3.204 r_angle_refined_deg 2.135 r_angle_other_deg 1.157 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.08 r_dihedral_angle_4_deg 20.782 r_dihedral_angle_3_deg 16.033 r_dihedral_angle_1_deg 7.002 r_mcangle_it 4.635 r_mcbond_it 3.22 r_mcbond_other 3.204 r_angle_refined_deg 2.135 r_angle_other_deg 1.157 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing