Experiment: 8BB0

X-RAY DIFFRACTION

Starting Model(s)

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

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 (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	6FFV	1.5	62.4	112532	5900	96.1	0.1446	0.143	0.15	0.1745	0.18	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.