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Crystal structure of the R116A mutant AhpE from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.5 M Na-malonate, 0.1 M Na-acetate, pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.26 α = 90 b = 147.26 β = 90 c = 33.303 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 PIXEL DECTRIS PILATUS 6M 2013-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.25 104 97.5 0.098 0.111 10.93 2.73 17069 -3 45.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 87 0.816 0.932 1.83
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 4X0X 2.25 104 16096 962 97.84 0.2104 0.2095 0.2102 0.2242 0.2254 RANDOM 40.799
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] -0.43 -0.43 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.296 r_dihedral_angle_3_deg 10.058 r_dihedral_angle_4_deg 9.55 r_dihedral_angle_1_deg 2.674 r_mcangle_it 1.704 r_angle_refined_deg 1.229 r_mcbond_it 0.927 r_mcbond_other 0.927 r_angle_other_deg 0.72 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.296 r_dihedral_angle_3_deg 10.058 r_dihedral_angle_4_deg 9.55 r_dihedral_angle_1_deg 2.674 r_mcangle_it 1.704 r_angle_refined_deg 1.229 r_mcbond_it 0.927 r_mcbond_other 0.927 r_angle_other_deg 0.72 r_chiral_restr 0.074 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2376 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Coot model building