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Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Tris-HCl, 0.8M Potassium sodium tartrate, 2.5% PEG 5000, MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 2 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris-HCl, 0.8M Potassium sodium tartrate, 0.75% PEG 5000, MME, 5mM K2PtCl4, 16h soaking, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.236 α = 90 b = 60.236 β = 90 c = 171.276 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 CCD RIGAKU JUPITER 210 Two dimensional focusing mirror 2005-04-16 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD RIGAKU JUPITER 210 Two dimensional focusing mirror 2005-05-25 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00000 SPring-8 BL26B1 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.07181, 1.07216, 1.05000 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.55 50 97.2 0.071 18.79 6.6 45583 -3 19.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.55 1.61 93.3 0.282 5.05 4.1 4258
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.55 42.82 44576 4520 95.1 0.182 0.1829 0.209 0.2099 RANDOM 20.7
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] -0.16 -0.16 0.32
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 4.75 c_scbond_it 3.54 c_mcangle_it 2.96 c_mcbond_it 2.34 c_angle_deg 1.6 c_improper_angle_d 1.15 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 4.75 c_scbond_it 3.54 c_mcangle_it 2.96 c_mcbond_it 2.34 c_angle_deg 1.6 c_improper_angle_d 1.15 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2113 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 42
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing