3T00

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


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 NaCl, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.123α = 90
b = 111.123β = 90
c = 72.441γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2010-12-20MSINGLE 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
11.8501000.05313.713.84264741825
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)
11.81.830.69312.1

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 3SZY1.82541726210398.110.20670.20490.2406RANDOM28.9543
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]
-0.16-0.160.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.734
r_dihedral_angle_4_deg12.898
r_dihedral_angle_3_deg12.777
r_dihedral_angle_1_deg5.159
r_scangle_it2.297
r_scbond_it1.335
r_angle_refined_deg1.114
r_mcangle_it1.099
r_mcbond_it0.596
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.734
r_dihedral_angle_4_deg12.898
r_dihedral_angle_3_deg12.777
r_dihedral_angle_1_deg5.159
r_scangle_it2.297
r_scbond_it1.335
r_angle_refined_deg1.114
r_mcangle_it1.099
r_mcbond_it0.596
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3184
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms8

Software

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