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Crystal structure of HMA (MMAA4) from mycobacterium tuberculosis complexed with S-adenosylhomocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FK8 PDB ENTRY 2FK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285 4-28% PEG 3350, pH 5-9, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.344 α = 90 b = 57.344 β = 90 c = 203.978 γ = 120
Symmetry Space Group P 31 2 1
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 2005-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 2.2 28.68 98.4 0.047 9.1 3.4 20193 20193 44.1
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 2.2 2.32 97.8 0.301 2.4 3.4 2844
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2FK8 2.2 28.68 19162 1031 97.82 0.20399 0.20164 0.25001 0.2674 RANDOM 57.076
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.853 r_dihedral_angle_4_deg 22.176 r_dihedral_angle_3_deg 15.763 r_dihedral_angle_1_deg 6.157 r_scangle_it 3.825 r_scbond_it 2.571 r_angle_refined_deg 1.674 r_mcangle_it 1.623 r_mcbond_it 1.003 r_symmetry_hbond_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.853 r_dihedral_angle_4_deg 22.176 r_dihedral_angle_3_deg 15.763 r_dihedral_angle_1_deg 6.157 r_scangle_it 3.825 r_scbond_it 2.571 r_angle_refined_deg 1.674 r_mcangle_it 1.623 r_mcbond_it 1.003 r_symmetry_hbond_refined 0.321 r_nbtor_refined 0.315 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.139 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2256 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling