2EWE

Crystal structure of Pectate Lyase C R218K mutant in complex with pentagalacturonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AIRpectate lyase C, PDB entry 1AIR, with arg 218 omitted

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.5277Grown in 1.0 M ammonium sulfate, 50 mM HEPES. VAPOR DIFFUSION, SITTING DROP, temperature 277K. Crystals then transferred to a solution at pH 9.5 containing cryogenic agents, 7 mM calcium and 50mM penta-galacturonopyranose, and left to soak for 30 hours.
Crystal Properties
Matthews coefficientSolvent content
3.5465.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.14α = 90
b = 78.32β = 90
c = 94.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103IMAGE PLATEMARRESEARCH1996-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.08SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.1523.7695.90.03111.8285232852322.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpectate lyase C, PDB entry 1AIR, with arg 218 omitted2.21022666226512263896.50.1860.233random13.4
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_angle_deg1.54
x_improper_angle_d1.17
x_bond_d0.0006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2646
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms53

Software

Software
Software NamePurpose
X-PLORrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing