1SWX | pdb_00001swx

Crystal structure of a human glycolipid transfer protein in apo-form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	PEG 3350, potassium phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.439	α = 90
b = 35.259	β = 115.82
c = 57.507	γ = 90

Symmetry
Space Group	P 1 21 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	2003-06-25	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418
2	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	1.65	50	97.5	0.063		4.6	23782	23776

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)
	1.65	1.68			0.34			1051

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.65	20	23167	22569	1202	97.42	0.1753	0.17536	0.17249	0.19	0.22567	0.24	RANDOM	26.075

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]
-1.06		-0.21	-0.19		1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.43
r_scangle_it	4.468
r_scbond_it	2.736
r_angle_refined_deg	1.694
r_mcangle_it	1.653
r_angle_other_deg	1.627
r_mcbond_it	0.903
r_symmetry_vdw_other	0.304
r_nbd_other	0.246
r_nbd_refined	0.245
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.164
r_nbtor_other	0.111
r_chiral_restr	0.083
r_symmetry_vdw_refined	0.028
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1605
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	6

Software

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