2EUM

Crystal structure of human Glycolipid Transfer Protein complexed with 8:0 Lactosylceramide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EUK	PDB ENTRY 2EUK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	293	15-20% PEG 3350 or 8000, 50 mM possium phosphate, pH 4.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.509	α = 90
b = 49.264	β = 122.57
c = 68.66	γ = 90

Symmetry
Space Group	C 1 2 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2005-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.3	20	99.9	0.095		3.6	9584	9562

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)
1	2.3	2.38	99.9		0.523		3.4	946

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	PDB ENTRY 2EUK	2.3	20	9584	9562	460	99.9	0.187	0.187	0.184	0.25	RANDOM	43.892

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]
-2.31		-0.58	0.83		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.43
r_dihedral_angle_4_deg	21.085
r_dihedral_angle_3_deg	16.031
r_dihedral_angle_1_deg	5.601
r_scangle_it	2.512
r_scbond_it	1.494
r_angle_refined_deg	1.259
r_mcangle_it	1.196
r_mcbond_it	0.669
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.43
r_dihedral_angle_4_deg	21.085
r_dihedral_angle_3_deg	16.031
r_dihedral_angle_1_deg	5.601
r_scangle_it	2.512
r_scbond_it	1.494
r_angle_refined_deg	1.259
r_mcangle_it	1.196
r_mcbond_it	0.669
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.17
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1645
Nucleic Acid Atoms
Solvent Atoms	153
Heterogen Atoms	70

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.