2YPO

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one site


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
3.9468.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.969α = 90
b = 203.969β = 90
c = 66.6γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2011-10-19MSINGLE 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
1244.1699.90.10.10211.55.31069362
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)
122.111000.470.471.65.4

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 3NV8244.16101510532599.830.139320.138290.1593RANDOM28.127
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]
4.654.65-9.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.655
r_dihedral_angle_4_deg19.011
r_dihedral_angle_3_deg14.161
r_dihedral_angle_1_deg6.287
r_angle_refined_deg2.002
r_angle_other_deg1.399
r_chiral_restr0.138
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.655
r_dihedral_angle_4_deg19.011
r_dihedral_angle_3_deg14.161
r_dihedral_angle_1_deg6.287
r_angle_refined_deg2.002
r_angle_other_deg1.399
r_chiral_restr0.138
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_bond_other_d0.007
r_gen_planes_other0.006
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 Atoms7037
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
CCP4phasing