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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 41.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.594 α = 90 b = 60.594 β = 90 c = 64.146 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 2003-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8124 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 1.85 52.49 99.8 0.078 20.2 11.2 11478 11478 -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 1.85 1.96 99.7 0.539 5 11.2 1821
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 1.85 20 11477 10863 614 99.84 0.1546 0.1538 0.1551 0.1688 0.1747 RANDOM 25.398
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] 0.67 0.33 0.67 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.671 r_dihedral_angle_4_deg 29.618 r_dihedral_angle_3_deg 12.472 r_dihedral_angle_1_deg 6.456 r_scangle_it 3.958 r_scbond_it 2.715 r_angle_refined_deg 1.812 r_mcangle_it 1.751 r_mcbond_it 1.115 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.671 r_dihedral_angle_4_deg 29.618 r_dihedral_angle_3_deg 12.472 r_dihedral_angle_1_deg 6.456 r_scangle_it 3.958 r_scbond_it 2.715 r_angle_refined_deg 1.812 r_mcangle_it 1.751 r_mcbond_it 1.115 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.203 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.129 r_metal_ion_refined 0.059 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 825 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing