2I3F | pdb_00002i3f

Crystal Structure of a Glycolipid transfer-like protein from Galdieria sulphuraria

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TFJ	FFAS03 homology model based on PDB 1tfj

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 M Tris PH 8.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (16% PEG 1.5K, 0.050 M HEPES pH 7.5) CRYOPROTECTED WITH WELL SOLUTION WITH 20% glycerol, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.438	α = 90
b = 48.195	β = 115.06
c = 89.411	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	MARMOSAIC 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2006-08-04	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97925	APS	22-ID
2

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	1.38	43.963	99.1	0.036	17.474	3.6		93177

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)
	1.38	1.43	92.4		0.246	3.754	2.9	8635

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	FFAS03 homology model based on PDB 1tfj	1.38	43.963	93176	4669	99.013	0.184	0.184	0.182	0.179	0.213	0.2083	RANDOM	19.835

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]
-0.324		0.129	0.427		0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.506
r_dihedral_angle_4_deg	14.928
r_dihedral_angle_3_deg	13.736
r_dihedral_angle_1_deg	4.799
r_scangle_it	4.453
r_scbond_it	2.984
r_mcangle_it	2.049
r_angle_refined_deg	1.781
r_mcbond_it	1.415
r_nbtor_refined	0.32
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.191
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.112
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3417
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction