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PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000144a
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 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.73 α = 90 b = 61.32 β = 90 c = 65.84 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 2017-03-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 1.56 48.73 99.5 0.038 0.042 0.017 1 20.2 6.3 28648
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 1.56 1.6 99.4 1.546 1.677 0.644 0.667 6.7 2086
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 1.56 44.87 27169 1421 99.4 0.2046 0.2023 0.2159 0.2521 0.2579 RANDOM 35.528
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.447 r_dihedral_angle_4_deg 21.926 r_dihedral_angle_3_deg 15.857 r_dihedral_angle_1_deg 6.344 r_mcangle_it 4.821 r_mcbond_it 3.475 r_mcbond_other 3.364 r_angle_refined_deg 2.18 r_angle_other_deg 1.209 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.447 r_dihedral_angle_4_deg 21.926 r_dihedral_angle_3_deg 15.857 r_dihedral_angle_1_deg 6.344 r_mcangle_it 4.821 r_mcbond_it 3.475 r_mcbond_other 3.364 r_angle_refined_deg 2.18 r_angle_other_deg 1.209 r_chiral_restr 0.154 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing