1SV3 | pdb_00001sv3

Structure of the complex formed between Phospholipase A2 and 4-methoxybenzoic acid at 1.3A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FB2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	297	0.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.57	α = 90
b = 52.57	β = 90
c = 47.823	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	203	CCD	MARRESEARCH	MIRROR	2003-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31		EMBL/DESY, HAMBURG	X31

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	1.3	20	94.1	0.119	8.8	8.7	28771	28771			19.4

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)
	1.3	1.36	99.4		0.42	2.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FB2	1.35	20	28771	25474	1364	93.28	0.2147	0.20986	0.20822	0.24267	RANDOM	20.353

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]
0.34			0.34		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.632
r_dihedral_angle_1_deg	3.417
r_scangle_it	3.112
r_scbond_it	2.15
r_angle_refined_deg	1.781
r_mcangle_it	1.771
r_mcbond_it	1.032
r_angle_other_deg	0.906
r_nbd_refined	0.438
r_symmetry_hbond_refined	0.243
r_nbd_other	0.21
r_symmetry_vdw_refined	0.196
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_other	0.176
r_xyhbond_nbd_other	0.156
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	944
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	36

Software

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