1YXH | pdb_00001yxh

Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong anticoagulant activity

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	10mM phosphate buffer, 2mM CaCl2, 25% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.817	α = 90
b = 42.817	β = 90
c = 65.994	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	293	IMAGE PLATE	MARRESEARCH	Mirror	2002-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	42.64	98			49325	9822

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.86	1.9	94.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.86	20	9349	9349	473	98.02	0.221	0.19608	0.19455	0.2251	RANDOM	27.03

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]
-0.19			-0.19		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.865
r_dihedral_angle_1_deg	2.683
r_scangle_it	2.416
r_scbond_it	1.434
r_angle_refined_deg	1.077
r_mcangle_it	1.047
r_mcbond_it	0.515
r_nbd_refined	0.297
r_symmetry_hbond_refined	0.24
r_symmetry_vdw_refined	0.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.865
r_dihedral_angle_1_deg	2.683
r_scangle_it	2.416
r_scbond_it	1.434
r_angle_refined_deg	1.077
r_mcangle_it	1.047
r_mcbond_it	0.515
r_nbd_refined	0.297
r_symmetry_hbond_refined	0.24
r_symmetry_vdw_refined	0.236
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.074
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	931
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.