2GNS

Design of specific peptide inhibitors of phospholipase A2: Crystal structure of the complex formed between a group II phospholipase A2 and a designed pentapeptide Ala- Leu- Val- Tyr- Lys at 2.3 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FB2	1FB2.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.2	298	0.2M ammonium sulphate, 30% PEG 4000, pH 7.2, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.14	α = 90
b = 53.14	β = 90
c = 48.53	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	288	IMAGE PLATE	MARRESEARCH	Mirror	2006-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	20	97.7			5989	5989			37.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.34	94.7

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-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FB2.pdb	2.3	18.79	5989	5924	336	97	0.21	0.21	0.197	0.212	RANDOM	30.8

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]
1.41			1.41		-2.82

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.9
c_scangle_it	2.56
c_angle_deg	2.2
c_mcangle_it	2.04
c_scbond_it	1.68
c_mcbond_it	1.18
c_improper_angle_d	1.13
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	985
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	5

Software

Software
Software Name	Purpose
CNS	refinement
AUTOMAR	data reduction
DENZO	data reduction
SCALEPACK	data scaling
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.