2JDD

Glyphosate N-acetyltransferase bound to acetyl COA and 3-phosphoglycerate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BSWPDB ENTRY 2BSW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6100 MM SODIUM ACETATE, PH 4.6 150-300 MM AMMONIUM SULFATE 20-25% PEG4000 2 MM ACETYL COA 20 MM D-3-PHOSPHOGLYCERATE
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.828α = 90
b = 48.448β = 103.57
c = 46.798γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

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
11.645.698.70.0341.13.319905
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)
11.61.6689.60.118.32.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2BSW1.645.641889910141000.1570.1550.193RANDOM13.54
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]
0.130.11-0.090.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.387
r_dihedral_angle_4_deg12.774
r_dihedral_angle_3_deg11.476
r_dihedral_angle_1_deg6.049
r_sphericity_free5.577
r_scangle_it3.078
r_scbond_it2.397
r_sphericity_bonded2.023
r_mcangle_it1.61
r_angle_refined_deg1.448
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.387
r_dihedral_angle_4_deg12.774
r_dihedral_angle_3_deg11.476
r_dihedral_angle_1_deg6.049
r_sphericity_free5.577
r_scangle_it3.078
r_scbond_it2.397
r_sphericity_bonded2.023
r_mcangle_it1.61
r_angle_refined_deg1.448
r_mcbond_it1.374
r_rigid_bond_restr1.289
r_angle_other_deg0.776
r_mcbond_other0.401
r_symmetry_vdw_other0.304
r_nbd_refined0.199
r_nbd_other0.198
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.161
r_symmetry_hbond_refined0.13
r_nbtor_other0.083
r_chiral_restr0.082
r_symmetry_vdw_refined0.055
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1161
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling