2X5X

The crystal structure of PhaZ7 at atomic (1.2 Angstrom) resolution reveals details of the active site and suggests a substrate binding mode


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VTVPDB ENTRY 2VTV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7289PHAZ7 WAS CRYSTALLIZED IN THE PRESENCE OF PMSF USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 16 C. THE WELL SOLUTION CONSISTED OF 20% W/V PEG3350 AND 0.2 M NA IODIDE AND A 0.1 M PMSF STOCK SOLUTION IN ISOPROPANOL WAS ADDED TO THE WELL TO A FINAL CONCENTRATION OF 10 MM.A 1.5 MICROLITER PROTEIN SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION ON SILICONIZED COVERSLIPS.
Crystal Properties
Matthews coefficientSolvent content
2.5752.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.63α = 90
b = 140.58β = 90
c = 56.75γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.22099.90.111.15.91247373.5
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)
11.21.2399.90.433.699.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 2VTV1.22098593950.13920.1390.176RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
163140
RMS Deviations
KeyRefinement Restraint Deviation
s_anti_bump_dis_restr0.519
s_approx_iso_adps0.091
s_non_zero_chiral_vol0.077
s_zero_chiral_vol0.073
s_similar_adp_cmpnt0.033
s_from_restr_planes0.0286
s_angle_d0.026
s_bond_d0.011
s_rigid_bond_adp_cmpnt0.004
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2549
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms29

Software

Software
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
PHASERphasing