3GCI

Crystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide at 2 A Resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	290	10mM Sodium phosphate, pH 6.0, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.679	α = 90
b = 42.679	β = 90
c = 65.817	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	2008-09-23	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	2.04	20	97.6	0.115	7.8		7596	7596

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	2.04	2.09	96.7		0.305	2.1

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 ENTRY 1MF4	2.04	19.51	7596	7065	340	97.91	0.19	0.18606	0.18436	0.22137	RANDOM	28.418

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]
-0.43			-0.43		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.77
r_dihedral_angle_3_deg	15.611
r_dihedral_angle_4_deg	13.796
r_dihedral_angle_1_deg	4.884
r_scangle_it	2.944
r_scbond_it	1.878
r_mcangle_it	1.408
r_angle_refined_deg	1.172
r_mcbond_it	0.732
r_symmetry_hbond_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.77
r_dihedral_angle_3_deg	15.611
r_dihedral_angle_4_deg	13.796
r_dihedral_angle_1_deg	4.884
r_scangle_it	2.944
r_scbond_it	1.878
r_mcangle_it	1.408
r_angle_refined_deg	1.172
r_mcbond_it	0.732
r_symmetry_hbond_refined	0.3
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.274
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.103
r_metal_ion_refined	0.013
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	949
Nucleic Acid Atoms
Solvent Atoms	93
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 National Science Foundation (DBI-1832184), 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.