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Crystal Structure of the precatalytic M-PMV dUTPase - substrate (dUPNPP) 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 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.596 α = 90 b = 60.596 β = 90 c = 63.862 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 BENT, VERTICALLY FOCUSING MIRROR 2005-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8034 EMBL/DESY, HAMBURG X13
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 1.6 20 99.2 0.04 17 2.7 17501 17501 -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 1.6 1.68 99.8 0.32 3.2 2.2 2371
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 1.6 20 16534 16534 966 99.22 0.16866 0.16698 0.1718 0.19733 0.2 RANDOM 31.095
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] 0.94 0.47 0.94 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.471 r_dihedral_angle_4_deg 24.465 r_dihedral_angle_1_deg 12.911 r_dihedral_angle_3_deg 11.885 r_scangle_it 7.401 r_scbond_it 5.358 r_mcangle_it 3.835 r_mcbond_it 2.908 r_angle_refined_deg 1.957 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.471 r_dihedral_angle_4_deg 24.465 r_dihedral_angle_1_deg 12.911 r_dihedral_angle_3_deg 11.885 r_scangle_it 7.401 r_scbond_it 5.358 r_mcangle_it 3.835 r_mcbond_it 2.908 r_angle_refined_deg 1.957 r_nbtor_refined 0.32 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.193 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.123 r_metal_ion_refined 0.082 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 823 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 29
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing