3G8H

Crystal structure of phospholipase A2 ammodytoxin C from vipera ammodytes ammodytes

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	1.2M (NH4)2SO4, 0.1M IMIDAZOLE, 0.2M (LI)2SO4, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.73	α = 90
b = 67.73	β = 90
c = 45.34	γ = 120

Symmetry
Space Group	P 3 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 315	MIRROR	2007-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97565	ESRF	ID23-1

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	1.35	45.33	96.5	0.084	0.084	6.7	10	25781	25781		-3	8.7

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	1.35	1.42	79.8		0.661	0.661	1.2	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZWP	1.35	45.33	25781	25781	1013	96.5	0.172	0.172	0.171	0.196	RANDOM	13.05

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]
-0.88	-0.44		-0.88		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.369
r_dihedral_angle_4_deg	17.577
r_dihedral_angle_3_deg	13.058
r_dihedral_angle_1_deg	5.261
r_scangle_it	2.999
r_scbond_it	2.193
r_mcangle_it	1.882
r_mcbond_it	1.559
r_angle_refined_deg	1.464
r_angle_other_deg	0.881
r_mcbond_other	0.308
r_nbd_refined	0.223
r_symmetry_vdw_other	0.204
r_symmetry_vdw_refined	0.192
r_nbtor_refined	0.19
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.117
r_nbtor_other	0.088
r_chiral_restr	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	954
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling