3H1X | pdb_00003h1x

Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.3M AMMONIUM SULPHATE, 30% PEG 4000 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.66	α = 90
b = 51.66	β = 90
c = 48.003	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	298	IMAGE PLATE	MARRESEARCH	Mirror	2006-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5414

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	51.99	99.2	0.045	19.5	19.7	24939	24939

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)
	1.4	1.42	100		0.418	2.9

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FB2	1.4	51.99	24939	24235	518	99.25	0.19042	0.19013	0.2	0.20661	0.22	RANDOM	21.888

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]
0.36			0.36		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.803
r_dihedral_angle_1_deg	4.7
r_scangle_it	3.152
r_angle_refined_deg	2.273
r_sphericity_free	2.081
r_scbond_it	2.066
r_sphericity_bonded	1.968
r_mcangle_it	1.821
r_rigid_bond_restr	1.252
r_mcbond_it	1.114
r_angle_other_deg	1.014
r_nbd_refined	0.406
r_nbd_other	0.249
r_symmetry_vdw_other	0.242
r_xyhbond_nbd_refined	0.189
r_symmetry_hbond_refined	0.154
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.107
r_xyhbond_nbd_other	0.028
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_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	1005
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	40

Software

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