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Crystal Structure Of Mycobacterium tuberculosis Guanylate Kinase In Complex With GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 15% (w/v) xylitol, 3.5M sodium chloride, 0.1M sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.046 α = 90 b = 113.046 β = 90 c = 113.046 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 2003-12-14 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 2.3 20 99.7 0.083 32.2 32.8 10829 10829 47
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 2.301 2.36 100 0.458 10.3 33.3 791
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 1ZNW 2.3 20 10834 10297 537 99.91 0.18641 0.18641 0.18392 0.1928 0.23581 0.1894 RANDOM 24.798
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 5.909 r_scangle_it 3.335 r_scbond_it 2.023 r_angle_refined_deg 1.572 r_mcangle_it 1.253 r_angle_other_deg 0.883 r_mcbond_it 0.667 r_nbd_other 0.231 r_symmetry_vdw_other 0.228 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.909 r_scangle_it 3.335 r_scbond_it 2.023 r_angle_refined_deg 1.572 r_mcangle_it 1.253 r_angle_other_deg 0.883 r_mcbond_it 0.667 r_nbd_other 0.231 r_symmetry_vdw_other 0.228 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.092 r_nbtor_other 0.081 r_symmetry_vdw_refined 0.043 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_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 1389 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling XSCALE data scaling CCP4 phasing