2EVD | pdb_00002evd

Crystal structure of human Glycolipid Transfer Protein complexed with 12:0 Lactosylceramide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.592	α = 90
b = 49.36	β = 122.38
c = 68.632	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	2004-12-09	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	20	100	0.058		7.2	14549	14549

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	2.07	100		0.602		6.8	1446

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 (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 2EUM	2	20	14549	14549	730	99.84	0.181	0.181	0.178	0.18	0.234	0.23	RANDOM	38.205

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]
-2.25		-0.66	1.12		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.972
r_dihedral_angle_4_deg	16.699
r_dihedral_angle_3_deg	15.085
r_dihedral_angle_1_deg	5.605
r_scangle_it	4.142
r_scbond_it	2.747
r_mcangle_it	1.866
r_angle_refined_deg	1.612
r_mcbond_it	1.194
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.972
r_dihedral_angle_4_deg	16.699
r_dihedral_angle_3_deg	15.085
r_dihedral_angle_1_deg	5.605
r_scangle_it	4.142
r_scbond_it	2.747
r_mcangle_it	1.866
r_angle_refined_deg	1.612
r_mcbond_it	1.194
r_nbtor_refined	0.316
r_xyhbond_nbd_refined	0.21
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.173
r_symmetry_vdw_refined	0.158
r_chiral_restr	0.117
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1643
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	71

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.