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Crystal structure of the F37H 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, SITTING DROP 7.5 293 0.2 M Sodium citrate tribasic, 0.1 M HEPES sodium, 30% v/v (+/-)-2-Methyl-2,4-pentanediol pH 7.5
mixed in 1:1 ratio with
30 mg/mL protein (in 20 mM HEPES sodium, 150 mM NaCl, pH 7.6)
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.3 α = 90 b = 63.3 β = 90 c = 159.45 γ = 90
Symmetry Space Group P 43 21 2
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 2015-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980 SOLEIL PROXIMA 1
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 1.45 44.76 97.8 0.074 0.077 18.54 11.7 57365 -3 30.077
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 1.45 1.49 81.5 0.886 0.963 1.88
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 1.45 44.76 55523 1729 98.01 0.1667 0.1657 0.176 0.1978 0.2011 RANDOM 27.638
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] -0.28 -0.28 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.018 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 12.276 r_dihedral_angle_1_deg 5.91 r_mcangle_it 1.809 r_angle_refined_deg 1.436 r_mcbond_it 1.18 r_mcbond_other 1.171 r_angle_other_deg 0.798 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.018 r_dihedral_angle_4_deg 15.988 r_dihedral_angle_3_deg 12.276 r_dihedral_angle_1_deg 5.91 r_mcangle_it 1.809 r_angle_refined_deg 1.436 r_mcbond_it 1.18 r_mcbond_other 1.171 r_angle_other_deg 0.798 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction