4X94

Crystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (hexagonal form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3	277	100 mM citric acid pH 3, 0.8 M ammonium sulfate ; crystallized in the presence of methyl arachidonyl fluorophosphonate

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.978	α = 90
b = 95.978	β = 90
c = 207.943	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2013-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97937	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.7	30	94.7	0.134	0.139	0.036	7.8	12.5		16438

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.74	92.4		0.75	0.78	0.203	0.905		11.6	765

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	4X90	2.7	30	15534	853	99.66	0.1793	0.177	0.2211	RANDOM	50.566

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]
1.09	0.54		1.09		-3.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.436
r_dihedral_angle_3_deg	15.236
r_dihedral_angle_4_deg	13.713
r_dihedral_angle_1_deg	6.437
r_mcangle_it	2.906
r_mcbond_it	1.752
r_mcbond_other	1.752
r_angle_refined_deg	1.408
r_angle_other_deg	0.806
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.436
r_dihedral_angle_3_deg	15.236
r_dihedral_angle_4_deg	13.713
r_dihedral_angle_1_deg	6.437
r_mcangle_it	2.906
r_mcbond_it	1.752
r_mcbond_other	1.752
r_angle_refined_deg	1.408
r_angle_other_deg	0.806
r_chiral_restr	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3019
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	96

Software

Software
Software Name	Purpose
HKL-2000	data scaling
SCALEPACK	data scaling
Aimless	data scaling
Coot	model building
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.