1OFP

CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE


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, 13-17MG/ML DAHPS
Crystal Properties
Matthews coefficientSolvent content
2.1342.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.59α = 106.38
b = 69.004β = 101.48
c = 102.45γ = 94.81
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATEMARRESEARCH2001-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
1219.997.40.05916.14.9414373
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)
12.032.1591.50.3643.32

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 1HFB2.119.8871709380098.60.2050.26RANDOM46.27
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_deg7.532
r_scangle_it7.278
r_scbond_it4.769
r_mcangle_it3.153
r_angle_refined_deg2.864
r_mcbond_it1.899
r_angle_other_deg1.25
r_symmetry_vdw_refined0.409
r_symmetry_vdw_other0.378
r_nbd_other0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.532
r_scangle_it7.278
r_scbond_it4.769
r_mcangle_it3.153
r_angle_refined_deg2.864
r_mcbond_it1.899
r_angle_other_deg1.25
r_symmetry_vdw_refined0.409
r_symmetry_vdw_other0.378
r_nbd_other0.26
r_nbd_refined0.238
r_xyhbond_nbd_refined0.216
r_chiral_restr0.198
r_symmetry_hbond_refined0.178
r_nbtor_other0.11
r_bond_refined_d0.043
r_gen_planes_refined0.015
r_gen_planes_other0.012
r_bond_other_d0.002
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 Atoms9225
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing