3JQL | pdb_00003jql

Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution

X-RAY DIFFRACTION

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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
2.04	39.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.023	α = 90
b = 42.023	β = 90
c = 64.146	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	2009-03-30	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	1.2	42	95.9	0.036	7.9		34924	34924

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)
	1.2	1.22	94.6		0.122	2.5

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	1.2	42	34924	31789	1695	96	0.18662	0.18076	0.21	0.19284	0.22	RANDOM	23.326

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.328
r_dihedral_angle_3_deg	14.809
r_dihedral_angle_1_deg	5.236
r_dihedral_angle_4_deg	3.568
r_scangle_it	2.501
r_sphericity_bonded	2.36
r_sphericity_free	2.175
r_scbond_it	1.907
r_rigid_bond_restr	1.337
r_mcangle_it	1.302
r_angle_refined_deg	1.164
r_mcbond_it	0.833
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.269
r_nbd_refined	0.214
r_chiral_restr	0.081
r_xyhbond_nbd_refined	0.081
r_symmetry_hbond_refined	0.077
r_metal_ion_refined	0.034
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	960
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	1

Software

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