3BIB | pdb_00003bib

Tim-4 in complex with phosphatidylserine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OR7	TIM-2 HOMOLOGOUS MODEL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	294	0.1 M SODIUM CITRATE, 10 % JEFFAMINE, 10 mM FeCl3. PROTEIN PRE-INCUBATED WITH 5 mM 1,2 DICAPROYL-sn-GLYCERO-3-(PHOSPHO-L-SERINE) AND 5 mM CaCl2, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.26	α = 90
b = 66.26	β = 90
c = 139.39	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97925	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	25	99.9	0.057	5.7	9.3	11	6801	6799

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.64	100		0.168	4.4	10.2

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	TIM-2 HOMOLOGOUS MODEL	2.5	15	6421	321	99.93	0.22082	0.21943	0.22	0.24831	0.25	RANDOM	36.021

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]
1.34	0.67		1.34		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.398
r_dihedral_angle_4_deg	18.573
r_dihedral_angle_3_deg	14.926
r_dihedral_angle_1_deg	6.214
r_rigid_bond_restr	6.153
r_scbond_it	5.219
r_scangle_it	4.125
r_sphericity_free	2.58
r_sphericity_bonded	2.283
r_mcangle_it	1.115
r_angle_refined_deg	1.114
r_mcbond_it	0.64
r_nbtor_refined	0.298
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.165
r_metal_ion_refined	0.148
r_symmetry_hbond_refined	0.111
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	855
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing