3RZN

Crystal Structure of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.1	273	20-25% PEG 8000, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.891	α = 90
b = 50.06	β = 118.52
c = 65.404	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	CCD	ADSC QUANTUM 315r		2009-09-11	M	SINGLE WAVELENGTH

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

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	1.1	50	99.8	0.08	19			96462		2

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	1.1	1.15	99.5		0.293	3.67

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1SWX	1.1	14.97	2	81298	4312	99.4	0.139	0.138	0.15	0.157	0.17	RANDOM	13

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]
-0.14		-0.2	-0.27		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.63
r_dihedral_angle_3_deg	13.997
r_dihedral_angle_4_deg	11.758
r_sphericity_free	7.385
r_dihedral_angle_1_deg	5.196
r_sphericity_bonded	4.616
r_scangle_it	4.298
r_scbond_it	3.318
r_mcangle_it	2.308
r_mcbond_it	2.016
r_angle_other_deg	1.881
r_rigid_bond_restr	1.713
r_angle_refined_deg	1.586
r_mcbond_other	0.802
r_symmetry_vdw_other	0.246
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.231
r_symmetry_hbond_refined	0.21
r_nbtor_refined	0.195
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.101
r_nbtor_other	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1660
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	61

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling