1OF6

crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae complexed with tyrosine and manganese


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HFBMOLECULE A OF PDB-CODE 1HFB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8.00
Crystal Properties
Matthews coefficientSolvent content
2.2445.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.129α = 64.71
b = 94.696β = 85.51
c = 104.843γ = 75.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2001-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.052096.50.06710.12.44071272.05
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.189.10.282.11.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMOLECULE A OF PDB-CODE 1HFB2.120151729494997.20.1950.237RANDOM43.66
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.931
r_scangle_it4.444
r_angle_other_deg3.888
r_scbond_it2.807
r_angle_refined_deg1.996
r_mcangle_it1.856
r_mcbond_it1.064
r_symmetry_hbond_refined0.372
r_nbd_other0.279
r_symmetry_vdw_other0.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.931
r_scangle_it4.444
r_angle_other_deg3.888
r_scbond_it2.807
r_angle_refined_deg1.996
r_mcangle_it1.856
r_mcbond_it1.064
r_symmetry_hbond_refined0.372
r_nbd_other0.279
r_symmetry_vdw_other0.274
r_nbd_refined0.218
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.177
r_chiral_restr0.12
r_nbtor_other0.114
r_bond_refined_d0.024
r_gen_planes_other0.01
r_gen_planes_refined0.008
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 AtomsNumber
Protein Atoms20826
Nucleic Acid Atoms
Solvent Atoms667
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing