☰ Navigation Tabs
Crystal Structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289 0.8M sodium formate, 15% PEG 4000, 0.2M sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.02 59.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 274.924 α = 90 b = 79.966 β = 112.44 c = 138.996 γ = 90
Symmetry Space Group C 1 2 1
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 2015-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.987 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.17 50 98.8 2.13 4 192931
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 1UXY 2.2 38.427 132792 6985 98.98 0.21 0.20739 0.2105 0.25939 0.2595 RANDOM 45.347
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.219 r_dihedral_angle_4_deg 18.793 r_dihedral_angle_3_deg 14.95 r_long_range_B_refined 8.432 r_long_range_B_other 8.428 r_dihedral_angle_1_deg 7.089 r_scangle_other 6.392 r_mcangle_other 5.576 r_mcangle_it 5.575 r_scbond_it 4.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.219 r_dihedral_angle_4_deg 18.793 r_dihedral_angle_3_deg 14.95 r_long_range_B_refined 8.432 r_long_range_B_other 8.428 r_dihedral_angle_1_deg 7.089 r_scangle_other 6.392 r_mcangle_other 5.576 r_mcangle_it 5.575 r_scbond_it 4.38 r_scbond_other 4.379 r_mcbond_it 3.967 r_mcbond_other 3.965 r_angle_refined_deg 1.938 r_angle_other_deg 1.093 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14778 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 321
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing