Experiment: 7R7J

Crystal structure of RadD with ADP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	277	20 mM Tris-HCl, 100 mM potassium chloride, 0.5 mM DTT, 0.5 mM magnesium chloride, 0.5 mM ATPgS, 9% (w/v) PEG 3350, 75 mM sodium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.415	α = 84.659
b = 74.449	β = 80.028
c = 109.4	γ = 82.769

Symmetry
Space Group	P 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 300 mm CCD		2019-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97856	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.03	45	90.5	0.105	0.124	0.066	0.983	10.1	3.3		79347			33.23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.1	60.7		1.105	1.378	0.81	0.39	0.1	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6DJE	2.03	35.65	0.08	71229	1812	80.96	0.2373	0.2364	0.2379	0.2694	0.2701	54.13

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	9.1549
f_angle_d	0.608
f_chiral_restr	0.0417
f_plane_restr	0.0047
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8846
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	60

Software

Software
Software Name	Purpose
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing
PHENIX	refinement