2D2G

OpdA from Agrobacterium radiobacter with bound product dimethylthiophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.627720% PEG 3350, 0.2M NaNO3, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7154.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.956α = 90
b = 108.956β = 90
c = 62.672γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173IMAGE PLATERIGAKU RAXIS IICConfocal mirrors2004-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5148

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.852597.73688935872
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9297.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8525341423251716250.1740.167420.166130.19367RANDOM16.04
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]
-0.96-0.48-0.961.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.758
r_dihedral_angle_4_deg13.949
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg6.03
r_scangle_it3.311
r_scbond_it2.081
r_angle_refined_deg1.3
r_mcangle_it1.108
r_mcbond_it0.72
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.758
r_dihedral_angle_4_deg13.949
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg6.03
r_scangle_it3.311
r_scbond_it2.081
r_angle_refined_deg1.3
r_mcangle_it1.108
r_mcbond_it0.72
r_nbtor_refined0.303
r_nbd_refined0.208
r_symmetry_hbond_refined0.182
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.126
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2511
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing