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PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z2212124043
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 2.51 50.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.201 α = 90 b = 60.331 β = 90 c = 65.785 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 1.95 28.88 99.4 0.054 0.059 0.023 0.999 19 6.5 14451
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 1.95 2 98.7 0.774 0.84 0.322 0.869 6.6 1040
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 1.95 44.5 13736 683 99.2 0.1927 0.1905 0.214 0.241 0.2587 RANDOM 43.336
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] 2.46 -1.99 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.354 r_dihedral_angle_4_deg 23.384 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_1_deg 5.961 r_mcangle_it 4.959 r_mcbond_it 3.355 r_mcbond_other 3.34 r_angle_refined_deg 1.745 r_angle_other_deg 1.069 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.354 r_dihedral_angle_4_deg 23.384 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_1_deg 5.961 r_mcangle_it 4.959 r_mcbond_it 3.355 r_mcbond_other 3.34 r_angle_refined_deg 1.745 r_angle_other_deg 1.069 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1193 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing