Experiment: 6QO9

Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis soaked with manganese ions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QO5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	1.8 - 2.0 M ammonium sulphate, 0.1 M Bis-Tris methane pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.529	α = 90
b = 61.231	β = 106.478
c = 95.836	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2014-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

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	1.299	28.7602449565	99	0.048	0.057	0.031	0.999	14.9	3.3		155351			10.749

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	1.3	1.35	97.65		0.532	0.632	0.338	0.796	2.16	3.3

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6QO5	1.299	28.76	1.353	155158	7756	98.95	0.137	0.136	0.1399	0.159	0.163	Random selection	17.981

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	20.8822998839
f_angle_d	1.20859176664
f_chiral_restr	0.0811594580925
f_bond_d	0.0120204894411
f_plane_restr	0.00759049329326

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4670
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	57

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement