1TJK | pdb_00001tjk

Crystal structure of the complex formed between group II phospholipase A2 with a designed pentapeptide, Phe- Leu- Ser- Thr- Lys at 1.2 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, SITTING DROP	6	293	Ammonium Sulphate, Polyethylene glycol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.293	α = 90
b = 52.293	β = 90
c = 47.83	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	2004-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8030	EMBL/DESY, HAMBURG	X11

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	1.25	20	100			35680	35680

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.25	1.28	99

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1SKG	1.25	51.99	35680	34764	916	99.98	0.18454	0.18406	0.20273	RANDOM	14.014

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]
0.04			0.04		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.488
r_dihedral_angle_1_deg	4.769
r_scangle_it	2.257
r_angle_refined_deg	1.725
r_scbond_it	1.461
r_mcangle_it	1.183
r_angle_other_deg	0.751
r_mcbond_it	0.625
r_nbd_refined	0.426
r_symmetry_vdw_other	0.285
r_xyhbond_nbd_refined	0.239
r_symmetry_vdw_refined	0.238
r_nbd_other	0.215
r_symmetry_hbond_refined	0.205
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	982
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	20

Software

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