2G58

Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZWP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	297	0.2M AMMONIUM SULPHATE, 50% PEG, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.588	α = 90
b = 52.588	β = 90
c = 47.848	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	203	CCD	MARRESEARCH	MIRROR	2003-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	0.803	EMBL/DESY, HAMBURG	X31

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	0.98	20	99.7	0.053	0.157	19.2	70330	70330

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.98	1	100		0.473	0.024

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	1ZWP	0.98	20	70330	69494	1390	93	0.133	0.1573	RANDOM	15.1

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 Method	Refinement High Resolution	Refinement Low Resolution
24	924	1266

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.113
s_non_zero_chiral_vol	0.104
s_approx_iso_adps	0.093
s_zero_chiral_vol	0.089
s_similar_adp_cmpnt	0.051
s_angle_d	0.033
s_from_restr_planes	0.032
s_bond_d	0.016
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	984
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
AMoRE	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.