Experiment: 8BB0

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	298	50 mM TRIS pH 7.8, 100 mM NaCl, 20 mM MgCl, 10 mM hydroxycobalamin, 33 % PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.11	α = 90
b = 101.099	β = 97.81
c = 79.893	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		2021-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9677	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.5	79.16	99.2	0.97	18.5	8		123287

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	7.4			0.95

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6FFV	1.5	62.4	112532	5900	96.1	0.1446	0.143	0.1745	RANDOM	15.922

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]
2.89		1.22	-2.79		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.512
r_dihedral_angle_1_deg	7.601
r_dihedral_angle_2_deg	7.507
r_rigid_bond_restr	5.698
r_angle_refined_deg	1.936
r_mcbond_it	1.357
r_mcangle_it	1.149
r_mcbond_other	0.893
r_angle_other_deg	0.581
r_chiral_restr	0.274

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.512
r_dihedral_angle_1_deg	7.601
r_dihedral_angle_2_deg	7.507
r_rigid_bond_restr	5.698
r_angle_refined_deg	1.936
r_mcbond_it	1.357
r_mcangle_it	1.149
r_mcbond_other	0.893
r_angle_other_deg	0.581
r_chiral_restr	0.274
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5247
Nucleic Acid Atoms
Solvent Atoms	508
Heterogen Atoms	360

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

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 R01GM133198.