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Crystal structure of M-PMV dUTPASE complexed with dUPNPP substrate
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 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.708 α = 90 b = 60.708 β = 90 c = 64.363 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2005-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8430 EMBL/DESY, HAMBURG BW7B
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 20 98.6 0.067 9.6 2.3 11407 11407 -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 1.95 100 0.515 2.1 2.3 1682
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 11353 10746 607 98.52 0.1704 0.1691 0.1727 0.1926 0.2017 RANDOM 29.651
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] 1.07 0.53 1.07 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.38 r_dihedral_angle_4_deg 30.488 r_dihedral_angle_3_deg 14.744 r_dihedral_angle_1_deg 12.924 r_scangle_it 6.401 r_scbond_it 5.001 r_mcangle_it 3.147 r_angle_refined_deg 2.035 r_mcbond_it 1.95 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.38 r_dihedral_angle_4_deg 30.488 r_dihedral_angle_3_deg 14.744 r_dihedral_angle_1_deg 12.924 r_scangle_it 6.401 r_scbond_it 5.001 r_mcangle_it 3.147 r_angle_refined_deg 2.035 r_mcbond_it 1.95 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.184 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.08 r_bond_refined_d 0.02 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 822 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing