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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.16	0.1889	0.19		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.