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Crystal structure of a MeaB- and MMAA-like GTPase from Mycobacterium tuberculosis bound to 2'-deoxyguanosine diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 289 MytuD.00200.a.A1 at 22 mg/mL with 4 mM dGTP against 0.1 M NaKHPO4, 48% PEG 200, 0.2 M NaCl, crystal tracking ID 236287b6, unique puck ID aqu7-6, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.66 53.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.92 α = 90 b = 187.82 β = 90 c = 66.46 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 ADSC QUANTUM 315r 2012-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 50 100 0.048 29.53 8.1 28351 28337 -3 36.499
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 2.05 100 0.465 4.66
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 3md0 2 45.45 28336 1431 99.95 0.1908 0.1889 0.1969 0.2269 0.2331 RANDOM 38.2709
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] 1.97 -1.37 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.771 r_dihedral_angle_4_deg 17.392 r_dihedral_angle_3_deg 12.75 r_dihedral_angle_1_deg 4.994 r_angle_refined_deg 1.514 r_angle_other_deg 0.832 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.771 r_dihedral_angle_4_deg 17.392 r_dihedral_angle_3_deg 12.75 r_dihedral_angle_1_deg 4.994 r_angle_refined_deg 1.514 r_angle_other_deg 0.832 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2198 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 48
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction