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Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and GDP. Northeast Structural Genomics Consortium target MaR46
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C3D PDB entry 3C3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 291 Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM Fo, 5 mM GDP, 5 mM MgCl2, 5 mM DTT. Reservoir solution: 100 mM HEPES pH 6.8, 0.5% PEG 8000, 1.35 M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.89 74.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.544 α = 90 b = 186.544 β = 90 c = 67.79 γ = 120
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 QUANTUM 315 Mirrors 2005-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.97926 NSLS X12C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3 28.69 92.6 0.093 0.073 12.13 3 49264 49264 84.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.11 90.3 0.368 0.345 1.5 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 3C3D 3 28.69 1 49264 39441 3958 74.7 0.206 0.206 0.2233 0.237 0.2601 RANDOM 84.9
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] -18.32 -18.32 36.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_angle_deg 1.2 c_improper_angle_d 0.85 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.1 c_angle_deg 1.2 c_improper_angle_d 0.85 c_bond_d 0.009 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9444 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 180
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling COMO phasing