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5-Mutant (R79W, R151A, E279A, E299A,E313A) Lactate-Dehydrogenase from Thermus thermophillus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V6M PDB ENTRY 2V6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 5-MUT TT-LDH WAS CRYSTALLIZED AT 10MG/ML BY THE HANGING-DROP VAPOUR-DIFFUSION METHOD, FOLLOWING THE MIXING OF THE PROTEIN AND THE MOTHER-LIQUOR SOLUTIONS AT A 1:1 RATIO. THE MOTHER LIQUOR SOLUTION WAS 0.1 M HEPES BUFFER PH 9, 18-20% PEG 6000, 2 M LICL2, 500 MICROMOLAR ADP. CRYSTALS GREW WITHIN A WEEK AT 4 DEGREES CELSIUS.
Crystal Properties Matthews coefficient Solvent content 2.76 55.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.123 α = 90 b = 59.597 β = 93.37 c = 153.076 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 100 CCD ADSC CCD 2009-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.9 45.53 96.8 0.103 14.25 3.47 30826 3 41.99
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 2.9 3 96.8 0.485 3.05 3.55
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 PDB ENTRY 2V6M 2.9 45.47 1.99 30812 2039 96.84 0.1919 0.1878 0.1863 0.2512 0.251
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] -0.2486 -3.2788 1.8068 -1.5582
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.057 f_angle_d 1.704 f_chiral_restr 0.107 f_plane_restr 0.016 f_bond_d 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9135 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing