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Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D4L PDB entry 2D4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.564 α = 90 b = 60.564 β = 90 c = 64.018 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm mirrors 2004-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8028, 1.0720 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.6 52.41 97.6 0.072 13.3 3.8 17234 17234 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 97 0.403 2.9 3 2584
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 rigid body refinement THROUGHOUT PDB entry 2D4L 1.6 20 17234 16305 929 97.61 0.1732 0.1722 0.1779 0.191 0.2012 RANDOM 25.406
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] 0.99 0.49 0.99 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.387 r_dihedral_angle_4_deg 26.211 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.031 r_scangle_it 5.321 r_scbond_it 4.261 r_mcangle_it 2.878 r_angle_refined_deg 1.952 r_mcbond_it 1.502 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.387 r_dihedral_angle_4_deg 26.211 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.031 r_scangle_it 5.321 r_scbond_it 4.261 r_mcangle_it 2.878 r_angle_refined_deg 1.952 r_mcbond_it 1.502 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.229 r_xyhbond_nbd_refined 0.185 r_symmetry_metal_ion_refined 0.167 r_chiral_restr 0.128 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 815 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing