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Structural insight into the enzymatic mechanism of the phophothreonine lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1W PDB entry 2P1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 12% PEG3350,0.1M MES pH6.0,0.1 M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.367 α = 90 b = 71.842 β = 90 c = 96.06 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2007-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 25.9 99.8 0.076 0.083 21 6.5 18132 10.4 107.8 19.484
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) 1 2 2.11 99.6 0.304 0.331 5.4 6.4 2578
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 2P1W 2 25.9 16331 16284 1846 99.71 0.18491 0.18491 0.1813 0.1784 0.21669 0.2153 RANDOM 16.817
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] -0.7 -0.81 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.19 r_dihedral_angle_4_deg 16.179 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_1_deg 5.629 r_scangle_it 1.894 r_scbond_it 1.198 r_angle_refined_deg 1.059 r_mcangle_it 0.893 r_mcbond_it 0.53 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.19 r_dihedral_angle_4_deg 16.179 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_1_deg 5.629 r_scangle_it 1.894 r_scbond_it 1.198 r_angle_refined_deg 1.059 r_mcangle_it 0.893 r_mcbond_it 0.53 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.18 r_nbd_refined 0.174 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1800 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASES phasing