3G8G | pdb_00003g8g

Crystal structure of phospholipase A2 ammodytoxin A from vipera ammodytes ammodytes

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	1.26M (NH4)2SO4, 0.1M TRIS, 0.2M (LI)2SO4, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.19	α = 90
b = 68.19	β = 90
c = 46.08	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	MARMOSAIC 225 mm CCD	MIRROR	2007-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2

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	1.7	29.527	99.9	0.143	0.143	4.7	10.4	13933	13933		-3	14.39

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	1.7	1.79	99.7		0.791	0.791	1	10.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZWP	1.7	29.527	13933	13933	531	99.9	0.174	0.174	0.172	0.18	0.216	0.22	RANDOM	12.71

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]
-0.7	-0.35		-0.7		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.632
r_dihedral_angle_4_deg	17.323
r_dihedral_angle_3_deg	12.785
r_dihedral_angle_1_deg	4.554
r_scangle_it	2.718
r_scbond_it	2
r_mcangle_it	1.697
r_mcbond_it	1.367
r_angle_refined_deg	1.193
r_angle_other_deg	0.825
r_mcbond_other	0.272
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.203
r_symmetry_hbond_refined	0.185
r_nbtor_refined	0.182
r_symmetry_vdw_other	0.174
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.17
r_nbtor_other	0.084
r_chiral_restr	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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	957
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	5

Software

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