3HSW | pdb_00003hsw

Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with 2-methoxycyclohexa-2-5-diene-1,4-dione

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P2P	PDB ENTRY 1P2P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	294	15% MPD, 0.05M Tris Maleate, 5mM Calcium Chloride, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.36	α = 90
b = 68.36	β = 90
c = 70.12	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	Mirrors	2009-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	45.24	97.3	0.073	0.065	8.5		6789	6759	2.5	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	70.79		0.073	0.065			955

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1P2P	2.5	13.65	2	2.5	6811	6356	349	98.44	0.2303	0.18214	0.17965	0.22	0.22883	0.22	RANDOM	23.783

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.295
r_dihedral_angle_4_deg	28.049
r_dihedral_angle_3_deg	22.792
r_dihedral_angle_1_deg	7.137
r_scangle_it	4.224
r_scbond_it	2.545
r_angle_refined_deg	2.079
r_mcangle_it	1.644
r_mcbond_it	0.84
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.295
r_dihedral_angle_4_deg	28.049
r_dihedral_angle_3_deg	22.792
r_dihedral_angle_1_deg	7.137
r_scangle_it	4.224
r_scbond_it	2.545
r_angle_refined_deg	2.079
r_mcangle_it	1.644
r_mcbond_it	0.84
r_chiral_restr	0.135
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	971
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MAR345dtb	data collection
Auto	model building
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
Auto	phasing

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.