1OFB

CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH MANGANESE(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, 2.4 EQUIV. MN, 13-17MG/ML DAHPS
Crystal Properties
Matthews coefficientSolvent content
1.9436.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 196.636α = 90
b = 50.502β = 106.36
c = 64.93γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray105IMAGE PLATEMARRESEARCHMIRRORS2001-07-15MSINGLE 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
122097.40.03215.981.8776999
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)
122.182.70.19093.821.46

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 1HFB2.0119.9238160200697.50.1610.207RANDOM28.99
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_deg5.941
r_scangle_it5.299
r_angle_other_deg3.705
r_scbond_it3.359
r_mcangle_it1.945
r_angle_refined_deg1.932
r_mcbond_it1.137
r_symmetry_vdw_other0.327
r_nbd_other0.294
r_symmetry_hbond_refined0.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.941
r_scangle_it5.299
r_angle_other_deg3.705
r_scbond_it3.359
r_mcangle_it1.945
r_angle_refined_deg1.932
r_mcbond_it1.137
r_symmetry_vdw_other0.327
r_nbd_other0.294
r_symmetry_hbond_refined0.257
r_nbd_refined0.225
r_xyhbond_nbd_refined0.155
r_chiral_restr0.141
r_symmetry_vdw_refined0.125
r_nbtor_other0.11
r_bond_refined_d0.023
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 Atoms5175
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing