3C86

OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D2JPDB ENTRY 2D2J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727720% PEG3350, 0.2M NaNO3, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0259.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.918α = 90
b = 108.918β = 90
c = 62.648γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICConfocal Mirrors2006-05-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.82098.93949139491
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.9193.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 2D2J1.8203748637486197798.850.16310.16310.161770.18683RANDOM24.42
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]
-1.42-0.71-1.422.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.159
r_dihedral_angle_4_deg17.57
r_dihedral_angle_3_deg12.867
r_dihedral_angle_1_deg6.846
r_scangle_it6.15
r_scbond_it4.305
r_mcangle_it2.596
r_mcbond_it1.991
r_angle_refined_deg1.596
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.159
r_dihedral_angle_4_deg17.57
r_dihedral_angle_3_deg12.867
r_dihedral_angle_1_deg6.846
r_scangle_it6.15
r_scbond_it4.305
r_mcangle_it2.596
r_mcbond_it1.991
r_angle_refined_deg1.596
r_nbtor_refined0.313
r_nbd_refined0.238
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.153
r_chiral_restr0.148
r_metal_ion_refined0.132
r_symmetry_hbond_refined0.104
r_bond_refined_d0.021
r_gen_planes_refined0.017
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_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 Atoms2504
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing