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Structure of the synthase subunit of PLP synthase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 PEG 8000, (NH4)2SO4, cacodylate, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.531 α = 90 b = 163.917 β = 90 c = 186.804 γ = 90
Symmetry Space Group C 2 2 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 CUSTOM-MADE mirrors 2005-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97951 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 99.9 125880 125880 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 2.2 49.94 1 125880 119560 6320 99.94 0.198 0.16117 0.15925 0.1588 0.19804 0.1964 RANDOM 40.211
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] 0.28 -0.97 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_4_deg 18.639 r_dihedral_angle_3_deg 15.465 r_dihedral_angle_1_deg 6.047 r_scangle_it 4.11 r_scbond_it 2.587 r_angle_refined_deg 1.564 r_mcangle_it 1.431 r_mcbond_it 0.896 r_symmetry_hbond_refined 0.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.378 r_dihedral_angle_4_deg 18.639 r_dihedral_angle_3_deg 15.465 r_dihedral_angle_1_deg 6.047 r_scangle_it 4.11 r_scbond_it 2.587 r_angle_refined_deg 1.564 r_mcangle_it 1.431 r_mcbond_it 0.896 r_symmetry_hbond_refined 0.352 r_symmetry_vdw_refined 0.347 r_nbtor_refined 0.306 r_xyhbond_nbd_refined 0.224 r_nbd_refined 0.212 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 11034 Nucleic Acid Atoms Solvent Atoms 1507 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 data scaling SHELXS phasing