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Crystal structure of GLMU from mycobacterium tuberculosis in complex with glucosamine-1-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 8% PEG 8000, 150MM NACL, 5% GLYCEROL, 1,3-BUTANEDIOL, AMPPNP, MGCL2, 0.1M HEPES, COCL2, DTT, pH 7.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.19 61.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.27 α = 90 b = 79.27 β = 90 c = 276.73 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 2009-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.6 19.932 99.4 0.088 20.1 19893 -3 42.49
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 2.6 2.67 94.9 0.602 2.86
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 3DJ4 2.6 19.93 19855 1011 99.5 0.202 0.199 0.1954 0.265 0.2629 RANDOM 33.01
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_4_deg 24.951 r_dihedral_angle_3_deg 18.041 r_dihedral_angle_1_deg 7.226 r_scangle_it 4.326 r_scbond_it 2.634 r_angle_refined_deg 1.979 r_mcangle_it 1.73 r_mcbond_it 0.928 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.034 r_dihedral_angle_4_deg 24.951 r_dihedral_angle_3_deg 18.041 r_dihedral_angle_1_deg 7.226 r_scangle_it 4.326 r_scbond_it 2.634 r_angle_refined_deg 1.979 r_mcangle_it 1.73 r_mcbond_it 0.928 r_chiral_restr 0.13 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3309 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling