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Crystal Structure Of Unliganded Form Of Mycobacterium tuberculosis Guanylate Kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S4Q PDB ENTRY 1S4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 15% (w/v) xylitol, 3.5M sodium chloride, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.04 α = 90 b = 112.04 β = 90 c = 112.04 γ = 90
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 ADSC QUANTUM 4 mirrors 2003-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9756 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.1 18.67 99.4 0.059 32.7 21.8 13765 13765 44.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.154 99.6 0.451 8.2 22 1028
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 (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 1S4Q 2.1 18.67 13778 13049 693 99.71 0.19346 0.19209 0.1895 0.21976 0.2034 RANDOM 24.749
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 34.13 r_dihedral_angle_4_deg 21.304 r_dihedral_angle_3_deg 16.743 r_dihedral_angle_1_deg 5.484 r_scangle_it 4.239 r_scbond_it 2.686 r_angle_refined_deg 1.405 r_mcangle_it 1.352 r_mcbond_it 1.219 r_angle_other_deg 0.801
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.13 r_dihedral_angle_4_deg 21.304 r_dihedral_angle_3_deg 16.743 r_dihedral_angle_1_deg 5.484 r_scangle_it 4.239 r_scbond_it 2.686 r_angle_refined_deg 1.405 r_mcangle_it 1.352 r_mcbond_it 1.219 r_angle_other_deg 0.801 r_nbtor_refined 0.3 r_symmetry_vdw_other 0.243 r_nbd_other 0.236 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.101 r_symmetry_hbond_refined 0.091 r_nbtor_other 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 1385 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling XSCALE data scaling CCP4 phasing