3NV8

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KGF3KGF (stripped of ligands and waters)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529520MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.9168.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 203.538α = 90
b = 203.538β = 90
c = 66.422γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++AXCO PX702009-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.2539.497.20.1188.36.1730377303733
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)
12.252.3395.40.4343.46.117137

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 REPLACEMENTTHROUGHOUT3KGF (stripped of ligands and waters)2.2539.3769535364897.410.181370.179970.208RANDOM36.915
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]
-0.18-0.09-0.180.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.064
r_dihedral_angle_4_deg19.658
r_dihedral_angle_3_deg17.497
r_dihedral_angle_1_deg7.335
r_scangle_it4.267
r_scbond_it2.991
r_angle_refined_deg2.157
r_mcangle_it1.963
r_mcbond_it1.181
r_angle_other_deg1.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.064
r_dihedral_angle_4_deg19.658
r_dihedral_angle_3_deg17.497
r_dihedral_angle_1_deg7.335
r_scangle_it4.267
r_scbond_it2.991
r_angle_refined_deg2.157
r_mcangle_it1.963
r_mcbond_it1.181
r_angle_other_deg1.148
r_mcbond_other0.32
r_chiral_restr0.126
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_gen_planes_other0.001
r_bond_other_d
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7098
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms69

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling