☰ Navigation Tabs
X-ray structure of the bifunctional 6-hydroxymethyl-7,8- dihydroxypterin pyrophosphokinase dihydropteroate synthase from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EYE PDB ENTRY 1EYE, PDB ENTRY 1CBK experimental model PDB 1CBK PDB ENTRY 1EYE, PDB ENTRY 1CBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.17 M NAH2PO4, 0.63 M K2HPO4, PH 6.3
Crystal Properties Matthews coefficient Solvent content 3.44 63.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.566 α = 90 b = 92.566 β = 90 c = 192.401 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU IMAGE PLATE AXCO MONOCAPILLARY OPTICS 2003-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.3 40 99.1 0.17 22.4 10.7 37688
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 91.1 0.85 3.8 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB ENTRY 1EYE, PDB ENTRY 1CBK 2.3 40 35738 1877 99.1 0.18 0.178 0.2102 0.216 0.2368 RANDOM 32.76
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] -0.13 -0.13 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.942 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 15.776 r_dihedral_angle_1_deg 5.77 r_scangle_it 5.433 r_mcangle_it 4.402 r_scbond_it 3.883 r_mcbond_it 3.111 r_angle_refined_deg 1.212 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.942 r_dihedral_angle_4_deg 19.109 r_dihedral_angle_3_deg 15.776 r_dihedral_angle_1_deg 5.77 r_scangle_it 5.433 r_mcangle_it 4.402 r_scbond_it 3.883 r_mcbond_it 3.111 r_angle_refined_deg 1.212 r_nbtor_refined 0.299 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4094 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing