Experiment: 5C8E

Crystal structure of Thermus thermophilus CarH bound to adenosylcobalamin and a 26-bp DNA segment

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C8A	3 different models were used for MR: residues 83-270 of PDB ID 5C8A; residues 6-75 of PDB ID 5C8F, and a model of a 26-bp DNA segment with ideal geometry, generated using 3D-DART
experimental model	PDB	5C8F	3 different models were used for MR: residues 83-270 of PDB ID 5C8A; residues 6-75 of PDB ID 5C8F, and a model of a 26-bp DNA segment with ideal geometry, generated using 3D-DART

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	16% PEG 3350, 0.2 M L-Proline, 0.1 M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.94	α = 90
b = 141.82	β = 90
c = 162.69	γ = 90

Symmetry
Space Group	P 21 21 2

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-F		2013-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9795	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3.89	100	99.9	0.098	15.7	12.2		38480

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.89	3.99	100		2	12.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3 different models were used for MR: residues 83-270 of PDB ID 5C8A; residues 6-75 of PDB ID 5C8F, and a model of a 26-bp DNA segment with ideal geometry, generated using 3D-DART	3.89	91.638	38338	1863	99.56	0.2505	0.2502	0.2583	0.2573	0.2614	Random selection	172

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	15.434
f_angle_d	0.789
f_chiral_restr	0.037
f_plane_restr	0.007
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14500
Nucleic Acid Atoms	2120
Solvent Atoms
Heterogen Atoms	872

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building