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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 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.333 α = 90 b = 60.333 β = 90 c = 64.519 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 1.65 20 97.9 0.04 15.4 2.3 15802 15802 -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 1.65 1.75 98.3 0.488 2.1 2.2
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 1.65 18.88 14564 14564 822 95.4 0.159 0.157 0.1618 0.182 0.1867 RANDOM 25.55
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] 0.99 0.49 0.99 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.172 r_dihedral_angle_4_deg 30.604 r_dihedral_angle_3_deg 14.289 r_scangle_it 8.905 r_dihedral_angle_1_deg 6.075 r_scbond_it 5.392 r_mcangle_it 2.842 r_angle_refined_deg 1.984 r_mcbond_it 1.678 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.172 r_dihedral_angle_4_deg 30.604 r_dihedral_angle_3_deg 14.289 r_scangle_it 8.905 r_dihedral_angle_1_deg 6.075 r_scbond_it 5.392 r_mcangle_it 2.842 r_angle_refined_deg 1.984 r_mcbond_it 1.678 r_nbtor_refined 0.322 r_nbd_refined 0.239 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.139 r_symmetry_hbond_refined 0.106 r_metal_ion_refined 0.049 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 830 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 45
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing