Experiment: 8DPB

MeaB in complex with the cobalamin-binding domain of its target mutase with GMPPCP bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	precipitant: 200 mM Lithium Chloride, 20% (w/v) PEG 3350; protein: 182 uM (20.2 mg/mL) complex in SEC buffer supplemented with 182 uM GMPPCP and 364 uM MgCl2); drop ratio: 150 nL of protein to 230 nL of precipitant solution

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.23	α = 90
b = 80.98	β = 90
c = 166.38	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2018-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9791	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.72	48.99	99.6	0.158	0.996	10.9	8.4		24685			49.55

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.72	2.84	99		0.689	0.804	2.5	8.4

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	in-house model	2.72	48.99	1.36	24626	1178	99.51	0.2172	0.2162	0.2171	0.2366	0.2382	51

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	20.9377
f_angle_d	0.906
f_chiral_restr	0.2742
f_bond_d	0.0116
f_plane_restr	0.0061

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6501
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	78

Software

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