3BKR | pdb_00003bkr

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
2.74	55.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63	α = 90
b = 63	β = 90
c = 67.8	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	93	CCD	MARMOSAIC 225 mm CCD		2006-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.90	APS	21-ID-D

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	1.4	25	98.3	0.062	23.3	7.4		30511			14.8

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)
	1.4	1.45	96.9		0.3	6.2	6.9	2946

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	Polyalanine model derived from 1PZ4	1.4	25	32038	30499	1539	98.33	0.188	0.186	0.19	0.219	0.22	RANDOM	17.419

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]
-0.01	-0.01		-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.292
r_dihedral_angle_4_deg	19.924
r_dihedral_angle_3_deg	12.005
r_dihedral_angle_1_deg	5.468
r_scangle_it	2.087
r_mcangle_it	1.805
r_scbond_it	1.39
r_angle_refined_deg	1.185
r_mcbond_it	1.131
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.292
r_dihedral_angle_4_deg	19.924
r_dihedral_angle_3_deg	12.005
r_dihedral_angle_1_deg	5.468
r_scangle_it	2.087
r_mcangle_it	1.805
r_scbond_it	1.39
r_angle_refined_deg	1.185
r_mcbond_it	1.131
r_nbtor_refined	0.317
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.206
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	974
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	18

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
HKL-2000	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.