3S0I | pdb_00003s0i

Crystal Structure of D48V mutant of Human Glycolipid Transfer Protein complexed with 3-O-sulfo galactosylceramide containing nervonoyl acyl chain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RZN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	273	20-25% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.315	α = 90
b = 47.454	β = 125.47
c = 63.257	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		2009-11-12	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	1.5	30	99.9	0.061	8.8	5.1		30330		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	1.5	1.55	99.9		0.444	2	3.2

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	3RZN	1.5	15	30330	28748	1469	99.53	0.15648	0.15408	0.15	0.20599	0.2	RANDOM	29.447

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]
-0.11		-0.09	0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.364
r_sphericity_free	27.668
r_sphericity_bonded	16.513
r_dihedral_angle_3_deg	14.264
r_dihedral_angle_4_deg	13.73
r_dihedral_angle_1_deg	4.872
r_scangle_it	4.429
r_scbond_it	3.502
r_rigid_bond_restr	3.211
r_mcangle_it	2.435
r_mcbond_it	2.108
r_angle_refined_deg	1.294
r_mcbond_other	0.847
r_symmetry_vdw_refined	0.298
r_symmetry_hbond_refined	0.28
r_symmetry_vdw_other	0.261
r_nbd_refined	0.24
r_nbd_other	0.193
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.168
r_nbtor_other	0.092
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_bond_other_d
r_angle_other_deg
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	1618
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	61

Software

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