☰ Navigation Tabs
Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O7C PDB ENTRY 2O7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 12.5% PEG6000, 0.25M ammonium sulfate, 0.2M MES, 0.5mM PLP, 0.5% 2-mercaptoethanol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.488 α = 90 b = 153.487 β = 90 c = 80.671 γ = 90
Symmetry Space Group P 21 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 RAYONIX MX225HE 2010-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 2.6 50 99.3 0.149 0.067 57780 57379 -3
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 2.6 2.64 98.7 0.638 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2O7C 2.61 29.28 57379 54542 2902 98.22 0.19395 0.19395 0.19076 0.1898 0.25329 0.2509 RANDOM 29.487
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.217 r_dihedral_angle_3_deg 20.1 r_dihedral_angle_4_deg 17.493 r_dihedral_angle_1_deg 6.532 r_scangle_it 3.669 r_scbond_it 2.244 r_angle_refined_deg 1.693 r_mcangle_it 1.634 r_mcbond_it 0.86 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.217 r_dihedral_angle_3_deg 20.1 r_dihedral_angle_4_deg 17.493 r_dihedral_angle_1_deg 6.532 r_scangle_it 3.669 r_scbond_it 2.244 r_angle_refined_deg 1.693 r_mcangle_it 1.634 r_mcbond_it 0.86 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11907 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling