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Crystal Structure of Guanylate Kinase from Mycobacterium tuberculosis (Rv1389)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 sodium formate, glycerol, Tris, sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.126 α = 90 b = 112.126 β = 90 c = 112.126 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 IMAGE PLATE RIGAKU RAXIS IV 2003-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
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 2.16 79.06 99.91 0.058 36.6 8.91 12112 12112
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 2.16 2.24 100 0.508 4.94 9.1 1270
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIRAS THROUGHOUT 2.16 79.06 12112 12112 642 99.91 0.17988 0.17988 0.17717 0.1816 0.23071 0.2357 RANDOM 36.464
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_1_deg 5.925 r_scangle_it 5.923 r_scbond_it 3.435 r_mcangle_it 2.173 r_angle_refined_deg 1.89 r_mcbond_it 1.201 r_angle_other_deg 0.987 r_symmetry_vdw_other 0.276 r_nbd_other 0.256 r_symmetry_hbond_refined 0.254
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.925 r_scangle_it 5.923 r_scbond_it 3.435 r_mcangle_it 2.173 r_angle_refined_deg 1.89 r_mcbond_it 1.201 r_angle_other_deg 0.987 r_symmetry_vdw_other 0.276 r_nbd_other 0.256 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.129 r_symmetry_vdw_refined 0.111 r_nbtor_other 0.086 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 1389 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MLPHARE phasing