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Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD and cobalamin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 291 0.1 M Bicine/Tris pH 8.1, 12% PEG 1000, 12% PEG 3350, 12% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulphate, 0.2% w/v biotin, 0.2% w/v phospho(enol)pyruvic acid monosodium salt hydrate, 0.2% w/v D-(+)-Melezitose hydrate, 0.2% w/v cobalamin and 0.02M HEPES sodium pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.855 α = 90 b = 164.855 β = 90 c = 260.242 γ = 120
Symmetry Space Group P 31 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 77 CCD ADSC QUANTUM 315r 2012-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953691 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.38 20.05 99.4 164364
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2.38 20.049 1.34 163475 8211 99.72 0.1591 0.1566 0.1562 0.2051 0.2033 34.398
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] -0.25 -0.12 -0.25 0.81
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.604 f_angle_d 1.343 f_chiral_restr 0.115 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24843 Nucleic Acid Atoms Solvent Atoms 2631 Heterogen Atoms 418
Software Software Software Name Purpose PHENIX refinement MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling Blu-Ice data collection