2FNX

Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M ammonoium sulfate, 30% PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.06	α = 90
b = 53.06	β = 90
c = 48.524	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	283	IMAGE PLATE	MARRESEARCH		2005-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.7	52.7	96.2			3181	3181

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.73	95

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.7	52.7	3181	3181	332	93.16	0.221	0.19337	0.18938	0.23098	RANDOM	44.879

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]
0.27			0.27		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.402
r_scangle_it	5.085
r_dihedral_angle_1_deg	2.881
r_scbond_it	2.875
r_angle_refined_deg	2.563
r_mcangle_it	2.246
r_mcbond_it	1.129
r_nbd_refined	0.411
r_symmetry_vdw_refined	0.35
r_xyhbond_nbd_refined	0.221

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.402
r_scangle_it	5.085
r_dihedral_angle_1_deg	2.881
r_scbond_it	2.875
r_angle_refined_deg	2.563
r_mcangle_it	2.246
r_mcbond_it	1.129
r_nbd_refined	0.411
r_symmetry_vdw_refined	0.35
r_xyhbond_nbd_refined	0.221
r_symmetry_hbond_refined	0.195
r_chiral_restr	0.11
r_bond_refined_d	0.014
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	973
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
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 R01GM133198.