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dUTPase from M. tuberculosis in complex with Stl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% PEG 10.000 and 0.1 M Na-Hepes pH7.5
Crystal Properties Matthews coefficient Solvent content 3.51 64.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.407 α = 90 b = 150.429 β = 98.85 c = 107.37 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2019-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.75 75.33 95.07 0.976 8.3 4.4 61491
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.821 0.586
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.75 75.328 61491 3102 95.069 0.204 0.20371 0.20069 0.2026 0.25875 0.2555 56.503
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] 0.3 -3.356 1.149 -0.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.003 r_dihedral_angle_3_deg 19.26 r_dihedral_angle_4_deg 19.24 r_lrange_it 8.98 r_lrange_other 8.98 r_dihedral_angle_1_deg 6.982 r_mcangle_it 6.42 r_mcangle_other 6.42 r_scangle_it 6.181 r_scangle_other 6.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.003 r_dihedral_angle_3_deg 19.26 r_dihedral_angle_4_deg 19.24 r_lrange_it 8.98 r_lrange_other 8.98 r_dihedral_angle_1_deg 6.982 r_mcangle_it 6.42 r_mcangle_other 6.42 r_scangle_it 6.181 r_scangle_other 6.18 r_mcbond_it 4.139 r_mcbond_other 4.139 r_scbond_it 3.959 r_scbond_other 3.959 r_angle_other_deg 2.418 r_angle_refined_deg 1.46 r_symmetry_nbd_other 0.223 r_nbd_refined 0.205 r_nbd_other 0.197 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.066 r_chiral_restr 0.057 r_symmetry_xyhbond_nbd_refined 0.056 r_bond_other_d 0.036 r_gen_planes_other 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12091 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing