Experiment: 3QBT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R2Q	pdb entry codes 1r2q 2qv2
experimental model	PDB	2QV2	pdb entry codes 1r2q 2qv2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.147	α = 90
b = 55.34	β = 91.93
c = 173.836	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 225 mm CCD		2009-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	47.378	98.3	0.055				99857

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	2	2.1	97		0.334	4.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry codes 1r2q 2qv2	2	47.378	99857	4996	98.27	0.2096	0.2079	0.2411	RANDOM	39.609

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]
-2.25		0.78	0.85		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.088
r_dihedral_angle_4_deg	20.549
r_dihedral_angle_3_deg	14.499
r_dihedral_angle_1_deg	4.919
r_scangle_it	4.164
r_scbond_it	2.706
r_mcangle_it	1.675
r_angle_refined_deg	1.412
r_mcbond_it	1.147
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.088
r_dihedral_angle_4_deg	20.549
r_dihedral_angle_3_deg	14.499
r_dihedral_angle_1_deg	4.919
r_scangle_it	4.164
r_scbond_it	2.706
r_mcangle_it	1.675
r_angle_refined_deg	1.412
r_mcbond_it	1.147
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.12
r_chiral_restr	0.099
r_metal_ion_refined	0.018
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9950
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	142

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	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.