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Crystal structure of M-PMV dUTPASE post-inversion product (dUMP) COMPLEX
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 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.714 α = 90 b = 60.714 β = 90 c = 63.775 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 2004-12-13 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 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 1.4 20 99.3 0.071 13.4 2.7 26148 26148 -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 1.4 1.48 99.8 0.417 2.6 2.2 4009
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 1.4 20 26108 24723 1385 99.15 0.1797 0.179 0.1826 0.193 0.1972 RANDOM 24.752
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] 0.72 0.36 0.72 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.024 r_dihedral_angle_4_deg 20.854 r_dihedral_angle_3_deg 11.68 r_scangle_it 6.193 r_dihedral_angle_1_deg 5.999 r_scbond_it 5.05 r_mcangle_it 3.56 r_mcbond_it 2.051 r_angle_refined_deg 2.028 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.024 r_dihedral_angle_4_deg 20.854 r_dihedral_angle_3_deg 11.68 r_scangle_it 6.193 r_dihedral_angle_1_deg 5.999 r_scbond_it 5.05 r_mcangle_it 3.56 r_mcbond_it 2.051 r_angle_refined_deg 2.028 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.249 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.235 r_xyhbond_nbd_refined 0.223 r_chiral_restr 0.14 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 818 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing