☰ Navigation Tabs
Human m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 0.1 M acetate pH 4.5
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.05 α = 90 b = 60.57 β = 90 c = 65.45 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 100 PIXEL DECTRIS PILATUS 6M 2016-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.63 38.73 99.9 0.088 11.3 6.5 24476
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.66 99.7 1.895 0.8 6.5
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 MOLECULAR REPLACEMENT THROUGHOUT 5j3t 1.63 38.73 23182 1244 99.74 0.21441 0.21187 0.2226 0.26178 0.2657 RANDOM 30.885
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] 1.94 -2.02 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.887 r_dihedral_angle_4_deg 16.225 r_dihedral_angle_3_deg 12.808 r_long_range_B_other 7.075 r_long_range_B_refined 7.062 r_dihedral_angle_1_deg 6.002 r_scangle_other 5.851 r_mcangle_it 4.073 r_mcangle_other 4.07 r_scbond_it 3.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.887 r_dihedral_angle_4_deg 16.225 r_dihedral_angle_3_deg 12.808 r_long_range_B_other 7.075 r_long_range_B_refined 7.062 r_dihedral_angle_1_deg 6.002 r_scangle_other 5.851 r_mcangle_it 4.073 r_mcangle_other 4.07 r_scbond_it 3.998 r_scbond_other 3.973 r_mcbond_it 3.007 r_mcbond_other 2.989 r_angle_refined_deg 2.028 r_angle_other_deg 1.084 r_chiral_restr 0.124 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1169 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing