3BKS | pdb_00003bks

Crystal Structure of Sterol Carrier Protein-2 like-3 (SCP2-L3) from Aedes Aegypti

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PZ4	Polyalanine model derived from 1PZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	296	2 microl protein at 10mg/ml was mixed with 2microl mother liquor consisting of 25% Peg 8000, 200mM AmSO4, 200mM AmF, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.3	α = 90
b = 63.3	β = 90
c = 68.4	γ = 120

Symmetry
Space Group	P 32 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	296		Bruker Proteum		2007-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	25	99.9	0.018	38.3	1.9	17937	9644			22.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.2	99		0.063	5.9	1.9	1232

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 (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	Polyalanine model derived from 1PZ4	2.1	25	9607	463	99.9	0.167	0.166	0.19	0.189	0.2	RANDOM	14.127

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]
0.03	0.01		0.03		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.35
r_dihedral_angle_4_deg	25.885
r_dihedral_angle_3_deg	15.201
r_dihedral_angle_1_deg	5.51
r_scangle_it	2.612
r_mcangle_it	2.173
r_scbond_it	1.645
r_mcbond_it	1.372
r_angle_refined_deg	1.318
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.35
r_dihedral_angle_4_deg	25.885
r_dihedral_angle_3_deg	15.201
r_dihedral_angle_1_deg	5.51
r_scangle_it	2.612
r_mcangle_it	2.173
r_scbond_it	1.645
r_mcbond_it	1.372
r_angle_refined_deg	1.318
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.226
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	961
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SAINT	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.