Experiment: 6BBZ

Room temperature neutron/X-ray structure of sisomicin bound AAC-VIa

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, 15-17% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.822	α = 90
b = 86.169	β = 94.55
c = 76.9	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++		2017-07-01	M	SINGLE WAVELENGTH
2	1	neutron	298	DIFFRACTOMETER	ORNL ANGER CAMERA		2017-07-01	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	NUCLEAR REACTOR	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0-4.0	ORNL Spallation Neutron Source	MANDI

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	1.9	50	99.25	0.047		0.067	0.047	0.997		17.2	1.66		25874			32.2
2	2.2	15.57	92.2	0.148		0.173	0.087	0.979		10.2	3.4		15860			32.2

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	1.9	1.97		0.401		0.511	0.313	0.839			2.1
1	1.97	2.05		0.321		0.406	0.246	0.886			2.4
1	2.05	2.14		0.243		0.307	0.185	0.926			2.4
1	2.14	2.25		0.165		0.208	0.125	0.963			2.4
1	2.25	2.39		0.127		0.161	0.097	0.978			2.4
1	2.39	2.58		0.089		0.112	0.067	0.989			2.4
1	2.58	2.84		0.065		0.081	0.049	0.992			2.4
1	2.84	3.25		0.045		0.056	0.033	0.996			2.4
1	3.25	4.09		0.031		0.038	0.023	0.998			2.5
1	4.09	50		0.031		0.038	0.023	0.997			2.4

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	1.9	38.329		1.34		25867	1286	99.23		0.1519	0.1503	0.1529	0.1814	0.1854
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.2	15.433				15512	763	92.47		0.1987	0.1976		0.2199

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	19.476
f_dihedral_angle_d	19.476
f_angle_d	0.81
f_angle_d	0.81
f_chiral_restr	0.074
f_chiral_restr	0.074
f_bond_d	0.013
f_bond_d	0.013
f_plane_restr	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2023
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	32

Software

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.