1YXL

Crystal structure of a novel phospholipase A2 from Naja naja sagittifera at 1.5 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	1mM CaCl2, 35% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.017	α = 90
b = 42.017	β = 90
c = 64.451	γ = 90

Symmetry
Space Group	P 41

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	MARRESEARCH	Mirror	2003-01-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	CU K-ALPHA	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.477	20.99		0.038	26.6	3.9	17781	17781			20.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.477	1.53	97.5		0.375	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1PSH	1.477	20	17781	17781	586	99.99	0.1904	0.18971	0.18842	0.22961	RANDOM	19.954

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]
-0.43			-0.43		0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.28
r_dihedral_angle_1_deg	3.958
r_scangle_it	2.955
r_scbond_it	1.979
r_angle_refined_deg	1.798
r_mcangle_it	1.203
r_angle_other_deg	1.076
r_mcbond_it	0.615
r_symmetry_hbond_refined	0.598
r_symmetry_vdw_refined	0.29
r_nbd_refined	0.281
r_symmetry_vdw_other	0.28
r_nbd_other	0.21
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.091
r_metal_ion_refined	0.038
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	913
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
AMoRE	phasing