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Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.02M MgCl2, 0.1M HEPES pH7.5, Polyacryslic acid 5100 sodium salt, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.94 68.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.589 α = 90 b = 112.589 β = 90 c = 68.818 γ = 120
Symmetry Space Group P 3 2 1
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 210r 2007-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B 1.123 PAL/PLS 6B
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 2.924 97.5 94.8 0.231 4.9 10571 10571 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.294 48.752 94.8 0.231 4.9 10571
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 2OBA 2.93 48.752 10068 10068 500 94.83 0.23 0.207 0.2041 0.2034 0.26503 0.2592 RANDOM 63.966
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] -2.98 -1.49 -2.98 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.479 r_dihedral_angle_3_deg 22.096 r_dihedral_angle_4_deg 15.549 r_dihedral_angle_1_deg 7.923 r_scangle_it 2.943 r_angle_refined_deg 2.029 r_scbond_it 1.839 r_mcangle_it 1.378 r_mcbond_it 0.719 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.479 r_dihedral_angle_3_deg 22.096 r_dihedral_angle_4_deg 15.549 r_dihedral_angle_1_deg 7.923 r_scangle_it 2.943 r_angle_refined_deg 2.029 r_scbond_it 1.839 r_mcangle_it 1.378 r_mcbond_it 0.719 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 1886 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling