1SX6 | pdb_00001sx6

Crystal structure of human Glycolipid Transfer protein in lactosylceramide-bound form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	PEG 8000, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.599	α = 90
b = 49.073	β = 122.52
c = 68.538	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 HTC	mirrors	2003-12-19	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	1.9	100	99.6	0.117	15	4.33	16853	16786

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	1.9	1.97			0.49	1.7		1672

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 (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 1SWX	1.95	20	14761	785	99.78	0.1947	0.19479	0.19202	0.2	0.24429	0.25	RANDOM	38.691

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]
-2.33		-0.23	1.27		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.398
r_scangle_it	3.135
r_scbond_it	1.821
r_mcangle_it	1.316
r_angle_refined_deg	1.24
r_angle_other_deg	0.845
r_mcbond_it	0.701
r_symmetry_hbond_refined	0.376
r_symmetry_vdw_refined	0.263
r_nbd_other	0.218
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_other	0.138
r_nbtor_other	0.088
r_chiral_restr	0.071
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1645
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	70

Software

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