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Crystal structure of K42A mutant of cystathionine beta-synthase from Lactobacillus plantarum in a complex with L-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q3D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 lithium sulfate, ammonium sulfate, sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.94 α = 90 b = 165.94 β = 90 c = 259.49 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 ADSC QUANTUM 315r 2014-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00 SPring-8 BL38B1
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 3.3 100 99.9 0.072 26.2 5.8 55046
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 3.3 3.42 100 0.498 3.8 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2q3d 3.3 29.98 2 53762 2714 97.7 0.238 0.238 0.2459 0.283 0.2883 RANDOM 45.6
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] -5.36 -5.36 10.71
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 2.7 c_mcangle_it 2.14 c_scbond_it 1.63 c_angle_deg 1.3 c_mcbond_it 1.21 c_improper_angle_d 0.67 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 27.2 c_scangle_it 2.7 c_mcangle_it 2.14 c_scbond_it 1.63 c_angle_deg 1.3 c_mcbond_it 1.21 c_improper_angle_d 0.67 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18120 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 272
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing