4X97 | pdb_00004x97

Crystal structure of Lysosomal Phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (MAFP)

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	7.5	277	100 mM HEPES pH 7.5, 3.5% PEG 8000, 28% MPD, 300 mM (NH4)2HPO4

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.147	α = 88.85
b = 85.495	β = 70.87
c = 88.852	γ = 79.74

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD		2013-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97857	APS	21-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	2.65	30	93.2	0.089	0.125	0.089	6.4	1.9		52162

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	2.65	2.7	4		0.573	0.81	0.573	0.222		1.2	111

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4X90	2.65	30	49603	2558	94.7	0.1813	0.1794	0.1851	0.2191	0.2194	RANDOM	39.398

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]
1.3	1.46	-0.29	-1	-0.7	0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.427
r_dihedral_angle_4_deg	15.994
r_dihedral_angle_3_deg	14.054
r_dihedral_angle_1_deg	6.16
r_mcangle_it	3.282
r_mcbond_it	2.018
r_mcbond_other	2.014
r_angle_refined_deg	1.788
r_angle_other_deg	1.262
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.427
r_dihedral_angle_4_deg	15.994
r_dihedral_angle_3_deg	14.054
r_dihedral_angle_1_deg	6.16
r_mcangle_it	3.282
r_mcbond_it	2.018
r_mcbond_other	2.014
r_angle_refined_deg	1.788
r_angle_other_deg	1.262
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.008
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12098
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	372

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.