2IQX | pdb_00002iqx

Rat Phosphatidylethanolamine-Binding Protein Containing the S153E Mutation in the Complex with o-Phosphorylethanolamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BD9	PDB ENTRY 1BD9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	277	10mM o-phosphorylethamine+ 2mM GTP crystallized in 0.1M Sodium Acetate trihydrate pH 4.5 and 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.50

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.971	α = 90
b = 57.211	β = 109.69
c = 80.886	γ = 90

Symmetry
Space Group	P 1 21 1

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	SBC-2	MIRRORS	2003-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	32.25	99.2	0.123	3.1	3.7		25715

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)
	2.21	2.29	94.1		0.276	1.8	2.5

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 (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 1BD9	2.2	32.24	24400	22343	2419	96.35	0.18957	0.18192	0.18	0.26104	0.25	RANDOM	14.515

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]
-0.67		0.45	0.13		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.11
r_dihedral_angle_3_deg	13.471
r_dihedral_angle_4_deg	13.3
r_mcangle_it	8.464
r_mcbond_it	5.765
r_dihedral_angle_1_deg	4.296
r_scangle_it	3.918
r_scbond_it	2.44
r_angle_refined_deg	1.374
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.168
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4367
Nucleic Acid Atoms
Solvent Atoms	573
Heterogen Atoms	24

Software

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