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PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with YW-FY-378
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 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.226 α = 90 b = 60.434 β = 90 c = 65.249 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 1.69 28.71 99 0.049 0.053 0.021 0.999 19.3 6.5 21675
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 1.69 1.74 97.3 0.853 0.943 0.392 0.765 5.6 1543
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 1.69 44.38 20587 1055 98.67 0.2006 0.1981 0.2177 0.2538 0.2571 RANDOM 34.21
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] 1.56 -1.83 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.764 r_dihedral_angle_4_deg 23.226 r_dihedral_angle_3_deg 15.68 r_dihedral_angle_1_deg 6.767 r_mcangle_it 4.506 r_mcbond_it 3.006 r_mcbond_other 2.995 r_angle_refined_deg 2.084 r_angle_other_deg 1.185 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.764 r_dihedral_angle_4_deg 23.226 r_dihedral_angle_3_deg 15.68 r_dihedral_angle_1_deg 6.767 r_mcangle_it 4.506 r_mcbond_it 3.006 r_mcbond_other 2.995 r_angle_refined_deg 2.084 r_angle_other_deg 1.185 r_chiral_restr 0.133 r_bond_refined_d 0.02 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 88 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing