☰ Navigation Tabs
Structure of 6-pyruvoyltetrahydropterin synthase
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 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.853 α = 90 b = 117.68 β = 90 c = 153.828 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 315r 2008-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A 1.000 PAL/PLS 4A
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 2.34 93.47 99.9 0.094 0.108 7.6 43356 43356 2 2
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 2.343 99.9 0.094 0.108 7.6 43356
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 3QN9 2.34 36.571 43356 41012 2172 99.6 0.23 0.2244 0.22207 0.215 0.26659 0.2545 RANDOM 54.988
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] -3.21 3.12 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_3_deg 18.443 r_dihedral_angle_4_deg 15.658 r_dihedral_angle_1_deg 7.198 r_scangle_it 3.958 r_scbond_it 2.781 r_angle_refined_deg 2.003 r_mcangle_it 1.695 r_mcbond_it 0.947 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_3_deg 18.443 r_dihedral_angle_4_deg 15.658 r_dihedral_angle_1_deg 7.198 r_scangle_it 3.958 r_scbond_it 2.781 r_angle_refined_deg 2.003 r_mcangle_it 1.695 r_mcbond_it 0.947 r_chiral_restr 0.13 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 5640 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 6
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling