1OFA

Crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with phosphoenolpyruvate and cobalt(ii)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HFBPDB ENTRY 1HFB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18TRIS PH 7.5-9.0 10 MM 20% PEG3400, 5% GLYCEROL, 4 EQUIV. PEP, 2.5 EQUIV. CO2+ 13-17MG/ML DAHPS
Crystal Properties
Matthews coefficientSolvent content
1.9436.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.21α = 90
b = 50.61β = 106.33
c = 64.98γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATEMARRESEARCHMIRRORS2000-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.0218.696.80.05315.13.2128877
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)
12.022.1586.80.283.52

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1HFB2.0217.5737403197197.10.1550.204RANDOM24.18
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.447
r_scangle_it5.643
r_scbond_it3.726
r_angle_other_deg3.669
r_angle_refined_deg2.305
r_mcangle_it2.102
r_mcbond_it1.241
r_symmetry_vdw_other0.339
r_nbd_other0.302
r_chiral_restr0.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.447
r_scangle_it5.643
r_scbond_it3.726
r_angle_other_deg3.669
r_angle_refined_deg2.305
r_mcangle_it2.102
r_mcbond_it1.241
r_symmetry_vdw_other0.339
r_nbd_other0.302
r_chiral_restr0.274
r_nbd_refined0.229
r_symmetry_vdw_refined0.216
r_symmetry_hbond_refined0.213
r_xyhbond_nbd_refined0.174
r_nbtor_other0.112
r_bond_refined_d0.031
r_gen_planes_other0.015
r_gen_planes_refined0.01
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 Atoms5152
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing