1JQ8

Design of specific inhibitors of phospholipase A2: Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Leu-Ala-Ile-Tyr-Ser at 2.0 resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FE7	PDB: 1FE7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.825	α = 90
b = 90.375	β = 90
c = 77.59	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	180	IMAGE PLATE	MARRESEARCH		1999-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.98	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	20	96.3	0.076	0.02	9.22	2.7	17914	17914			31.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	90.3		4.3	0.17	9.4	2.1	1605

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	PDB: 1FE7	2	11.94	17841	17841	861	96.6	0.189	0.187	0.187	0.198	RANDOM	38.7

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]
0.49			-1.13		0.64

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.3
c_scangle_it	4.77
c_scbond_it	3.54
c_mcangle_it	3.16
c_improper_angle_d	2.71
c_angle_deg	2.2
c_mcbond_it	2.08
c_bond_d	0.032
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1928
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	17

Software

Software
Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement