3JQ5 | pdb_00003jq5

Phospholipase A2 Prevents the Aggregation of Amyloid Beta Peptides: Crystal Structure of the Complex of Phospholipase A2 with Octapeptide Fragment of Amyloid Beta Peptide, Asp-Ala-Glu-Phe-Arg-His-Asp-Ser at 2 A Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MF4	PDB ENTRY 1MF4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	290	calcium chloride, sodium phosphate, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.795	α = 90
b = 42.795	β = 90
c = 65.832	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	300	IMAGE PLATE	MARRESEARCH	MIRROR	2009-01-13	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)	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	2.03	20	98.7	0.07	11.1		7735	7735

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)
	2.03	2.06	87.7		0.188	4.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MF4	2.03	20	7735	7256	351	98.86	0.18458	0.18188	0.2	0.22063	0.24	RANDOM	24.881

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]
-0.5			-0.5		1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.818
r_dihedral_angle_3_deg	15.48
r_dihedral_angle_4_deg	14.415
r_dihedral_angle_1_deg	5.061
r_scangle_it	2.77
r_scbond_it	1.908
r_mcangle_it	1.412
r_angle_refined_deg	1.137
r_mcbond_it	0.739
r_symmetry_hbond_refined	0.453

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.818
r_dihedral_angle_3_deg	15.48
r_dihedral_angle_4_deg	14.415
r_dihedral_angle_1_deg	5.061
r_scangle_it	2.77
r_scbond_it	1.908
r_mcangle_it	1.412
r_angle_refined_deg	1.137
r_mcbond_it	0.739
r_symmetry_hbond_refined	0.453
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.283
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.103
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	977
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

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.