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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 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.559 α = 90 b = 60.559 β = 90 c = 63.635 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 2003-02-09 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2003-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8028 EMBL/DESY, HAMBURG X13 2 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0720 ESRF ID14-4
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 1,2 1.75 20 99.8 0.032 44.8 11.4 13399 13399 -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) 1,2 1.75 1.77 100 0.402 4.4 11.3 438
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 SIRAS THROUGHOUT PDB entry 2D4L 1.75 20 13305 12600 705 99.03 0.1536 0.1517 0.1529 0.1864 0.1883 RANDOM 27.004
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] 0.79 0.4 0.79 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.517 r_dihedral_angle_4_deg 28.651 r_dihedral_angle_3_deg 15.274 r_scangle_it 9.959 r_scbond_it 6.941 r_dihedral_angle_1_deg 5.745 r_mcangle_it 3.509 r_mcbond_it 2.722 r_angle_refined_deg 1.957 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.517 r_dihedral_angle_4_deg 28.651 r_dihedral_angle_3_deg 15.274 r_scangle_it 9.959 r_scbond_it 6.941 r_dihedral_angle_1_deg 5.745 r_mcangle_it 3.509 r_mcbond_it 2.722 r_angle_refined_deg 1.957 r_nbtor_refined 0.325 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.17 r_chiral_restr 0.118 r_metal_ion_refined 0.099 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 831 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SCALA data scaling SOLVE phasing