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Crystal structure of Mycobacterium tuberculosis LeuA complexed with citrate and Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HPS PDB entry 3HPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.25 291 Sodium citrate, PEG MME 2000, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.05 40.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.361 α = 90 b = 154.803 β = 98.04 c = 69.115 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 345 mm plate Osmic 2007-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5417
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 1.7 50 94.6 0.052 22.7 3.3 117445 117445
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 1.7 1.76 68.8 0.349 2.3 8508
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 PDB entry 3HPS 1.7 38.69 111160 111160 5974 94.68 0.17208 0.17208 0.17038 0.1703 0.20366 0.2037 RANDOM 18.941
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] 0.49 0.24 -0.28 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.63 r_dihedral_angle_4_deg 14.671 r_dihedral_angle_3_deg 12.452 r_dihedral_angle_1_deg 5.628 r_scangle_it 3.068 r_scbond_it 1.95 r_angle_refined_deg 1.288 r_mcangle_it 1.278 r_mcbond_it 0.765 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.63 r_dihedral_angle_4_deg 14.671 r_dihedral_angle_3_deg 12.452 r_dihedral_angle_1_deg 5.628 r_scangle_it 3.068 r_scbond_it 1.95 r_angle_refined_deg 1.288 r_mcangle_it 1.278 r_mcbond_it 0.765 r_nbtor_refined 0.305 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 8694 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 35
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing