4DBK

Crystal structure of porcine pancreatic phospholipase A2 complexed with berberine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	0.05M Tris maleate buffer, 5mM CaCl2, 16% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.6	α = 90
b = 68.6	β = 90
c = 70.08	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2009-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	49	98.1				7686

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 4P2P	2.3	9.9	7686	391	93.16	0.18767	0.18455	0.25313	RANDOM	45.444

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			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.398
r_dihedral_angle_4_deg	28.948
r_dihedral_angle_3_deg	19.241
r_dihedral_angle_1_deg	6.741
r_scangle_it	4.056
r_scbond_it	2.558
r_angle_refined_deg	1.796
r_mcangle_it	1.698
r_mcbond_it	0.907
r_chiral_restr	0.114
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	971
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	27

Software

Software
Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling