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Crystal structure of arginine/ornithine transport system ATPase from Mycobacterium tuberculosis bound to GDP (a RAS-like GTPase superfamily protein)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QM7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 289 50% PEG 200, 0.2 M NaCl, 0.1 M Na K phosphate pH 6.2, 22.0 mg/mL protein, 2 mM GDP, crystal tracking ID 207391d3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.63 53.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.53 α = 90 b = 187.36 β = 90 c = 66.2 γ = 90
Symmetry Space Group C 2 2 21
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 RIGAKU SATURN 944 2010-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.45 19.96 99.4 0.072 20.5 6.84 15339 -3 50.04
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 2.45 2.51 97.2 0.573 2.7 4.62
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2qm7 2.45 19.96 15268 780 98.96 0.213 0.211 0.2071 0.251 0.2187 RANDOM 45.656
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] 1.29 -1.08 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_4_deg 23.123 r_dihedral_angle_3_deg 17.826 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.025 r_scbond_it 2.374 r_angle_refined_deg 1.556 r_mcangle_it 1.497 r_mcbond_it 0.794 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_4_deg 23.123 r_dihedral_angle_3_deg 17.826 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.025 r_scbond_it 2.374 r_angle_refined_deg 1.556 r_mcangle_it 1.497 r_mcbond_it 0.794 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 32
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction