4X95 | pdb_00004x95

Crystal structure of fully glycosylated 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	3.5	297	100 mM Na citrate pH 3.5-4, 20% PEG 3350, and 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.385	α = 90
b = 125.275	β = 90
c = 140.215	γ = 90

Symmetry
Space Group	P 2 21 21

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	0.97933	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	3.08	30	49.4	0.173	0.19	0.076	4.2	5.1		12079

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	3.1	3.15	4.5		0.342	0.423	0.244	0.783		2.6	54

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	3.08	30	11420	615	49.49	0.2195	0.2177	0.2	0.2517	0.24	RANDOM	150.015

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]
42.72			-17.63		-25.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.967
r_dihedral_angle_3_deg	14.549
r_dihedral_angle_4_deg	11.182
r_dihedral_angle_1_deg	4.998
r_mcangle_it	4.455
r_mcbond_it	2.627
r_mcbond_other	2.626
r_angle_refined_deg	1.02
r_angle_other_deg	0.746
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.967
r_dihedral_angle_3_deg	14.549
r_dihedral_angle_4_deg	11.182
r_dihedral_angle_1_deg	4.998
r_mcangle_it	4.455
r_mcbond_it	2.627
r_mcbond_other	2.626
r_angle_refined_deg	1.02
r_angle_other_deg	0.746
r_chiral_restr	0.073
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6041
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	176

Software

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