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Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli complexed sepiapterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.16M tri-ammonium citrate pH 7.0, 16% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.714 α = 90 b = 115.882 β = 90 c = 155.185 γ = 90
Symmetry Space Group I 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 ADSC QUANTUM 210 2009-05-22 M SINGLE WAVELENGTH 2 1 CCD ADSC QUANTUM 210 2007-10-24
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.000 PAL/PLS 6C1 2 SYNCHROTRON PAL/PLS BEAMLINE 6B 1.1123 PAL/PLS 6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.496 92.851 99.9 0.069 14.3 35585 35585 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 2.496 92.851 99.9 0.069 7.3 35585
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 (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 3QN9 2.5 92.85 35585 35585 33805 0.18399 0.1816 0.179 0.23029 0.2206 RANDOM 25.15
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] -1.04 1.25 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.023 r_dihedral_angle_3_deg 17.42 r_dihedral_angle_4_deg 15.205 r_dihedral_angle_1_deg 6.852 r_scangle_it 4.759 r_scbond_it 3.076 r_angle_refined_deg 1.922 r_mcangle_it 1.896 r_mcbond_it 0.959 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.023 r_dihedral_angle_3_deg 17.42 r_dihedral_angle_4_deg 15.205 r_dihedral_angle_1_deg 6.852 r_scangle_it 4.759 r_scbond_it 3.076 r_angle_refined_deg 1.922 r_mcangle_it 1.896 r_mcbond_it 0.959 r_chiral_restr 0.134 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 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 5658 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 108
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling