1MF4

Structure-based design of potent and selective inhibitors of phospholipase A2: Crystal structure of the complex formed between phosholipase A2 from Naja Naja sagittifera and a designed peptide inhibitor at 1.9 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LN8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	295	sodium phosphate, CaCl2, ethanol; Co-crystallation of protein: peptide in 1:10 molar ratio, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.779	α = 90
b = 42.779	β = 90
c = 65.866	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	290	IMAGE PLATE	MARRESEARCH	MONOCHROMATOR	2001-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.9	20	93.2	0.073	19.3	1.04		8247		-3	20.63

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	1.9	1.97	61.3		0.289	1.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1LN8	1.9	19.54	8247	8247	411	100	0.184	0.182	0.239	RANDOM	25.5

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]
-0.24			-0.24		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.004
r_dihedral_angle_3_deg	17.004
r_scangle_it	3.903
r_dihedral_angle_1_deg	3.468
r_scbond_it	2.472
r_mcangle_it	1.769
r_angle_refined_deg	1.748
r_mcbond_it	0.88
r_symmetry_hbond_refined	0.689
r_symmetry_vdw_refined	0.449
r_nbd_refined	0.292
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.109
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	950
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement