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Crystal Structure of M-PMV dUTPase complexed with dUPNPP, substrate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 293.0K
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.071 α = 90 b = 61.071 β = 90 c = 64.357 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 MARRESEARCH 2004-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8128 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.52 52.93 98.72 0.076 0.057 12.34 2.66 20787 20787 -3 25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.61 98.23 0.442 0.334 2.86 2.13 3282
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 (All) 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 2D4L 1.53 20 19296 19296 1097 98.97 0.16566 0.16566 0.16443 0.169 0.18717 0.193 from starting model 22.778
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] 0.61 0.3 0.61 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_4_deg 30.573 r_dihedral_angle_3_deg 11.11 r_scangle_it 10.457 r_scbond_it 8.097 r_dihedral_angle_1_deg 5.752 r_mcangle_it 3.883 r_mcbond_it 2.624 r_angle_refined_deg 1.911 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_4_deg 30.573 r_dihedral_angle_3_deg 11.11 r_scangle_it 10.457 r_scbond_it 8.097 r_dihedral_angle_1_deg 5.752 r_mcangle_it 3.883 r_mcbond_it 2.624 r_angle_refined_deg 1.911 r_nbtor_refined 0.315 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.218 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.172 r_chiral_restr 0.141 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_metal_ion_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 826 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling