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Crystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-n-acetylglucosamine and pyrophosphate Snapshot 2
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, SITTING DROP 7.5 8% PEG 8000, 150MM NACL, 5% GLYCEROL, 1,3-BUTANEDIOL,AMPPNP, MGCL2,0.1M HEPES, COCL2, DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.98 58.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.58 α = 90 b = 76.58 β = 90 c = 276.97 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 2.04 19.94 99.2 0.067 22.35 38438 -3 35.49
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 2.04 2.09 94.1 0.604 3.24
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 2.04 19.94 38392 1007 99.3 0.181 0.18 0.1824 0.23 0.2319 RANDOM 30.9
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.434 r_dihedral_angle_4_deg 22.318 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 6.694 r_scangle_it 5.674 r_scbond_it 3.632 r_mcangle_it 2.191 r_angle_refined_deg 2.177 r_mcbond_it 1.297 r_chiral_restr 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.434 r_dihedral_angle_4_deg 22.318 r_dihedral_angle_3_deg 15.513 r_dihedral_angle_1_deg 6.694 r_scangle_it 5.674 r_scbond_it 3.632 r_mcangle_it 2.191 r_angle_refined_deg 2.177 r_mcbond_it 1.297 r_chiral_restr 0.256 r_bond_refined_d 0.027 r_gen_planes_refined 0.011 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 3374 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling