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N-acetyl glucosamine 1-phosphate uridyltransferase from Mycobacterium tuberculosis complex with N-acetyl glucosamine 1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HM9 PDB entry 1HM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2M Lithium nitrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.02 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.303 α = 90 b = 94.303 β = 90 c = 288.041 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 110 IMAGE PLATE MAR scanner 345 mm plate osmic 2007-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.75 42.33 100 0.151 13.2 6.3 13239 13239
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 100 0.623 3 6.3 1892
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 (All) 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 PDB entry 1HM9 2.75 40.42 12588 12588 651 99.95 0.19791 0.19791 0.19514 0.1922 0.25071 0.2463 RANDOM 27.107
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] -0.65 -0.32 -0.65 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.028 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 16.716 r_dihedral_angle_1_deg 7.136 r_scangle_it 2.599 r_angle_refined_deg 1.673 r_scbond_it 1.611 r_mcangle_it 1.14 r_mcbond_it 0.631 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.028 r_dihedral_angle_4_deg 19.322 r_dihedral_angle_3_deg 16.716 r_dihedral_angle_1_deg 7.136 r_scangle_it 2.599 r_angle_refined_deg 1.673 r_scbond_it 1.611 r_mcangle_it 1.14 r_mcbond_it 0.631 r_nbtor_refined 0.315 r_nbd_refined 0.238 r_symmetry_hbond_refined 0.211 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2795 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling PHASER phasing