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Structure of heme-degrader, MhuD (Rv3592), from Mycobacterium tuberculosis with two hemes bound in its active site
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.1 M Bis-Tris pH 5.0, 0.2 M NaCl, 20% PEG-3350, 10 mM triethylamine HCl
, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.91 35.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.971 α = 90 b = 64.622 β = 90.01 c = 71.082 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 70 CCD ADSC QUANTUM 315r Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing). 2008-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97, 1.76 SSRL BL7-1
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 1.75 50 98.9 0.066 28.1 19968
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) 1.75 1.81 98.6 0.165 10.7 1974
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 19.35 18936 1018 98.87 0.18856 0.18623 0.1853 0.23119 0.2299 RANDOM 22.804
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] -0.37 0.01 0.11 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.265 r_dihedral_angle_4_deg 16.771 r_dihedral_angle_3_deg 15.313 r_dihedral_angle_1_deg 6.629 r_scangle_it 5.586 r_scbond_it 3.649 r_mcangle_it 2.435 r_angle_refined_deg 2.01 r_mcbond_it 1.382 r_chiral_restr 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.265 r_dihedral_angle_4_deg 16.771 r_dihedral_angle_3_deg 15.313 r_dihedral_angle_1_deg 6.629 r_scangle_it 5.586 r_scbond_it 3.649 r_mcangle_it 2.435 r_angle_refined_deg 2.01 r_mcbond_it 1.382 r_chiral_restr 0.161 r_bond_refined_d 0.022 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 174
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling