1OFO

Crystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae in Complex with 2-Phosphoglycolate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18pH 8.00
Crystal Properties
Matthews coefficientSolvent content
1.9637.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.457α = 90
b = 50.955β = 106.41
c = 64.976γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2001-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEROTATING ANODE (CU)

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
11.8617.395.40.044419.773.8198507
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)
11.861.9589.10.30354.363.1

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 1HFB (MOLECULE A)1.8617.347358249395.60.1650.209RANDOM25.62
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_deg5.808
r_scangle_it5.015
r_angle_other_deg3.705
r_scbond_it3.114
r_mcangle_it1.871
r_angle_refined_deg1.728
r_mcbond_it1.047
r_nbd_other0.292
r_symmetry_vdw_other0.285
r_nbd_refined0.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.808
r_scangle_it5.015
r_angle_other_deg3.705
r_scbond_it3.114
r_mcangle_it1.871
r_angle_refined_deg1.728
r_mcbond_it1.047
r_nbd_other0.292
r_symmetry_vdw_other0.285
r_nbd_refined0.227
r_symmetry_hbond_refined0.223
r_chiral_restr0.136
r_xyhbond_nbd_refined0.134
r_symmetry_vdw_refined0.116
r_nbtor_other0.108
r_bond_refined_d0.02
r_gen_planes_other0.009
r_gen_planes_refined0.007
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 Atoms5165
Nucleic Acid Atoms
Solvent Atoms403
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing