2R1L

OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727720% PEG 3350, 0.2M sodium nitrate, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0159.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.923α = 90
b = 108.923β = 90
c = 62.647γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICConfocal Mirrors2006-10-24MSINGLE 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
11.952099.33154731298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.952.0796.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2D2J1.95203147729774150299.360.156040.154030.19654RANDOM20.31
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]
-1.16-0.58-1.161.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.477
r_dihedral_angle_4_deg17.01
r_dihedral_angle_3_deg14.029
r_dihedral_angle_1_deg7.11
r_scangle_it6.957
r_scbond_it5.008
r_mcangle_it2.816
r_mcbond_it2.344
r_angle_refined_deg1.638
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.477
r_dihedral_angle_4_deg17.01
r_dihedral_angle_3_deg14.029
r_dihedral_angle_1_deg7.11
r_scangle_it6.957
r_scbond_it5.008
r_mcangle_it2.816
r_mcbond_it2.344
r_angle_refined_deg1.638
r_nbtor_refined0.311
r_nbd_refined0.236
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.157
r_chiral_restr0.149
r_symmetry_hbond_refined0.102
r_metal_ion_refined0.044
r_bond_refined_d0.022
r_gen_planes_refined0.019
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 Atoms2511
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing