1S8G

Crystal structure of Lys49-Phospholipase A2 from Agkistrodon contortrix laticinctus, fatty acid bound form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3	58.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.897	α = 90
b = 81.897	β = 90
c = 49.902	γ = 90

Symmetry
Space Group	P 41 21 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	IMAGE PLATE	MAR scanner 345 mm plate	mirror	2001-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.544	LNLS	D03B-MX1

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	2.3	57.3	98.1	0.118	0.118		6.2	7960	7960		1.7

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	2.3	2.41	99.7		0.118	0.118	1.7	6.2

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	1PPA	2.3	57.3	7387	356	97.29	0.20663	0.20457	0.21	0.24721	0.25	RANDOM	41.135

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]
-1.72			-1.72		3.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.673
r_scangle_it	1.169
r_angle_refined_deg	0.929
r_angle_other_deg	0.726
r_scbond_it	0.672
r_mcangle_it	0.491
r_mcbond_it	0.247
r_symmetry_vdw_other	0.225
r_nbd_other	0.194
r_nbd_refined	0.169
r_symmetry_vdw_refined	0.146
r_xyhbond_nbd_refined	0.131
r_symmetry_hbond_refined	0.131
r_nbtor_other	0.082
r_chiral_restr	0.051
r_bond_refined_d	0.005
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	972
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing