6HMK

POLYADPRIBOSYL GLYCOHYDROLASE IN COMPLEX WITH PDD00016690


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A0D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293750 nL purified protein at 7.5 mg/mL in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT was mixed with 250 nL of seed stock and 1000 nL of a precipitant consisting of 18-23 % (w/v) PEG-3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5. Seed stock was prepared using a Seed BeadTM (Hampton Research) from a co-crystal of GS-PARG(448-976 [K617A, Q618A, K619A, E688A, K689A, K690A]) with ADP-ribose, with co-crystallisation mother liquor (19 % (w/v) PEG-3350, 0.2 M ammonium sulphate, 0.1 M PCTP pH 7.5) as the stabilising solution. The final volume of the seed stock was 100 microL.
Crystal Properties
Matthews coefficientSolvent content
2.4750.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.09α = 90
b = 90.11β = 90
c = 95.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

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
12.0634.831000.09211.45.93654027.39
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)
12.062.161000.5973.26.1

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 REPLACEMENTTHROUGHOUT4A0D2.0628.7736386182399.70.15540.15360.1888RANDOM33.03
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]
6.21423.0208-9.235
RMS Deviations
KeyRefinement Restraint Deviation
OTHER TORSION ANGLES16.45
PEPTIDE OMEGA TORSION ANGLES3.43
BOND ANGLES0.96
BOND LENGTHS0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4028
Nucleic Acid Atoms
Solvent Atoms448
Heterogen Atoms62

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PHASERphasing