3T02

Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoacetate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SZYPDB ENTRY 3SZY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529820% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.354α = 90
b = 111.354β = 90
c = 72.77γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-DAPS21-ID-D

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
125099.40.0758.911.231372
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)
122.0794.30.4745.52931

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3SZY22531290157999.440.19080.18860.2341RANDOM32.5197
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.717
r_dihedral_angle_4_deg15.277
r_dihedral_angle_3_deg13.885
r_dihedral_angle_1_deg5.714
r_scangle_it2.669
r_scbond_it1.563
r_mcangle_it1.289
r_angle_refined_deg1.191
r_mcbond_it0.701
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.717
r_dihedral_angle_4_deg15.277
r_dihedral_angle_3_deg13.885
r_dihedral_angle_1_deg5.714
r_scangle_it2.669
r_scbond_it1.563
r_mcangle_it1.289
r_angle_refined_deg1.191
r_mcbond_it0.701
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3182
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms10

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MD2data collection
PHASERphasing