2EWE | pdb_00002ewe

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AIR	pectate lyase C, PDB entry 1AIR, with arg 218 omitted

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	277	Grown 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 coefficient	Solvent content
3.54	65.22

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	MARRESEARCH		1996-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.08	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.15	23.76	95.9	0.031	11.8		28523	28523			22.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pectate lyase C, PDB entry 1AIR, with arg 218 omitted	2.2	10	2	26662	26512	2638	96.5	0.186	0.17	0.233	0.21	random	13.4

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
Key	Refinement Restraint Deviation
x_angle_deg	1.54
x_improper_angle_d	1.17
x_bond_d	0.0006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2646
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	53

Software

Software
Software Name	Purpose
X-PLOR	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.