3NJU

Crystal structure of the complex of group I phospholipase A2 with 4-Methoxy-benzoicacid at 1.4A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	10MM sodium phosphate buffer, 2M calcium chloride, 35% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.074	α = 90
b = 42.074	β = 90
c = 64.253	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	77	CCD	MARRESEARCH	Mirror	2010-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.4	42	96.5	0.063	79.9		22095	22095			19.1

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	1.4	1.42	95		0.448	5.5

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	1OXR	1.4	19.09	22095	20236	1102	96.59	0.17742	0.17673	0.17424	0.22388	RANDOM	25.03

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]
-0.21			-0.21		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.654
r_dihedral_angle_3_deg	13.516
r_dihedral_angle_4_deg	10.31
r_sphericity_free	7.819
r_sphericity_bonded	6.052
r_dihedral_angle_1_deg	5.855
r_scangle_it	4.602
r_mcangle_it	3.976
r_scbond_it	3.645
r_mcbond_it	3.101
r_rigid_bond_restr	2.807
r_angle_refined_deg	1.693
r_nbtor_refined	0.321
r_symmetry_vdw_refined	0.318
r_symmetry_hbond_refined	0.278
r_nbd_refined	0.262
r_xyhbond_nbd_refined	0.24
r_chiral_restr	0.112
r_metal_ion_refined	0.08
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	910
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	12

Software

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