Experiment: 6BBR

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6BC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	285	0.1 M Tris, pH 8.5, 0.3 M magnesium chloride, 15-18% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.6	α = 90
b = 86.1	β = 94
c = 78.8	γ = 90

Symmetry
Space Group	I 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	298	IMAGE PLATE	RIGAKU RAXIS IV++		2017-08-01	M	SINGLE WAVELENGTH
2	1	neutron	298	DIFFRACTOMETER	ORNL ANGER CAMERA		2017-08-01	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	ROTATING ANODE	RIGAKU MICROMAX-003	2.0-4.0

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	50	97.4	0.059		0.07	0.037			19.7	3.4		22336			38.7
2	2.3	15	83.8	0.167						7.8	2.4		12800			38.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07		0.489		0.582	0.311	0.834			3.4
1	2.07	2.15		0.391		0.462	0.244	0.888			3.5
1	2.15	2.25		0.285		0.338	0.18	0.926			3.4
1	2.25	2.37		0.203		0.241	0.128	0.955			3.5
1	2.37	2.52		0.153		0.181	0.096	0.978			3.5
1	2.52	2.71		0.108		0.128	0.068	0.986			3.5
1	2.71	2.99		0.079		0.093	0.049	0.991			3.5
1	2.99	3.42		0.057		0.067	0.036	0.992			3.5
1	3.42	4.31		0.045		0.054	0.029	0.992			3.4
1	4.31	50		0.042		0.05	0.027	0.993			3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.002	30.944		1.34		22336	1126	96.32		0.1598	0.1582	0.1889		54.6199
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.3	15				14029	708	89.39		0.222	0.2206	0.2458

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.593
f_angle_d	0.934
f_chiral_restr	0.065
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2028
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

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.