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Crystal Structure of DCP2 (NUDT20) after initial refinement with no ligand modelled (structure $n)
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 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.23 α = 90 b = 61.198 β = 90 c = 66.037 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 2017-07-27 M 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 1.66 29.06 99.8 0.042 0.046 0.018 0.999 21.4 6.5 23655
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 1.66 1.71 98.3 0.837 0.911 0.357 0.821 6.4 1691
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 1.66 44.89 22456 1150 99.77 0.1988 0.197 0.197 0.236 0.2359 RANDOM 31.935
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] -0.07 0.03 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.976 r_dihedral_angle_4_deg 17.793 r_dihedral_angle_3_deg 14.329 r_dihedral_angle_1_deg 5.935 r_scbond_it 4.001 r_mcangle_it 3.745 r_mcbond_it 2.593 r_angle_refined_deg 1.769 r_chiral_restr 0.146 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.976 r_dihedral_angle_4_deg 17.793 r_dihedral_angle_3_deg 14.329 r_dihedral_angle_1_deg 5.935 r_scbond_it 4.001 r_mcangle_it 3.745 r_mcbond_it 2.593 r_angle_refined_deg 1.769 r_chiral_restr 0.146 r_bond_refined_d 0.019 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1195 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing