2PH4

Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	polyethylene glycol 8,000; ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.933	α = 90
b = 72.933	β = 90
c = 93.938	γ = 120

Symmetry
Space Group	P 64

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	MAR CCD 165 mm		2007-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.05	23.87	99.5	0.071	33.4	12.5		17731		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.12	99.4		0.33	2.8	9.5

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 1Y4L	2.05	23.87	15931	1800	99.51	0.21729	0.20942	0.2886	RANDOM	29.077

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]
0.98	0.49		0.98		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.521
r_dihedral_angle_3_deg	19.202
r_dihedral_angle_4_deg	15.45
r_dihedral_angle_1_deg	13.676
r_scangle_it	4.163
r_scbond_it	3.068
r_angle_refined_deg	2.223
r_mcangle_it	1.829
r_mcbond_it	1.127
r_nbtor_refined	0.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.521
r_dihedral_angle_3_deg	19.202
r_dihedral_angle_4_deg	15.45
r_dihedral_angle_1_deg	13.676
r_scangle_it	4.163
r_scbond_it	3.068
r_angle_refined_deg	2.223
r_mcangle_it	1.829
r_mcbond_it	1.127
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.309
r_nbd_refined	0.245
r_symmetry_vdw_refined	0.234
r_xyhbond_nbd_refined	0.223
r_chiral_restr	0.138
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1940
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.