1TK4 | pdb_00001tk4

Crystal structure of russells viper phospholipase A2 in complex with a specifically designed tetrapeptide Ala-Ile-Arg-Ser at 1.1 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.2M AMMONIUM SULPHATE, 30% PEG , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.512	α = 90
b = 52.512	β = 90
c = 48.088	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	MARRESEARCH	mirror	2004-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.806	EMBL/DESY, HAMBURG	X11

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	1.1	50	100	0.041	22.9	9.7	52995	52995			10.4

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)
	1.1	1.12	100		0.381	3.5		2642

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1SKG	1.1	37.01	52429	529	100	0.16844	0.16826	0.18532	RANDOM	13.854

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]
0.13			0.13		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.83
r_scangle_it	2.738
r_sphericity_free	2.517
r_sphericity_bonded	2.403
r_scbond_it	1.808
r_mcangle_it	1.645
r_angle_refined_deg	1.519
r_mcbond_it	1.008
r_rigid_bond_restr	0.939
r_angle_other_deg	0.774
r_nbd_refined	0.425
r_nbd_other	0.241
r_symmetry_vdw_refined	0.238
r_symmetry_vdw_other	0.225
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.174
r_nbtor_other	0.086
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	993
Nucleic Acid Atoms
Solvent Atoms	197
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing