2YPP

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with 3 tyrosine molecules


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NV8PDB ENTRY 3NV8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
3.9268.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.449α = 90
b = 203.449β = 90
c = 66.49γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.347.03970.130.12610.77.6679612
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4286.70.240.2373.13.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3NV82.344.0264572338096.940.140460.139230.16375RANDOM29.829
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]
-4.42-4.428.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.868
r_dihedral_angle_4_deg20.469
r_dihedral_angle_3_deg15.267
r_dihedral_angle_1_deg6.5
r_angle_refined_deg2.058
r_angle_other_deg0.942
r_chiral_restr0.119
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.868
r_dihedral_angle_4_deg20.469
r_dihedral_angle_3_deg15.267
r_dihedral_angle_1_deg6.5
r_angle_refined_deg2.058
r_angle_other_deg0.942
r_chiral_restr0.119
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms7072
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling