8JBT | pdb_00008jbt

B12-binding domain from Chloracidobacterium thermophilum MerR family protein, anaerobic light state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1M Tris pH 8.5, 20% v/v Ethanol

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.485	α = 90
b = 123.485	β = 90
c = 73.105	γ = 120

Symmetry
Space Group	P 31 2 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 EIGER2 XE 16M		2022-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.299	106.941	100	0.2803	0.287	1	8.08	20.6		28905

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	99.9		2.463	2.75	0.5	0.72	19.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	THROUGHOUT	2.3	106.94	27458	1426	99.99	0.20733	0.20636	0.2073	0.22527	0.2273	RANDOM	45.694

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]
-0.17	-0.08		-0.17		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.498
r_dihedral_angle_2_deg	7.837
r_long_range_B_other	7.223
r_long_range_B_refined	7.222
r_dihedral_angle_1_deg	7.043
r_scangle_other	5.791
r_mcangle_it	4.208
r_mcangle_other	4.207
r_scbond_it	3.939
r_scbond_other	3.938
r_mcbond_it	2.933
r_mcbond_other	2.901
r_angle_refined_deg	0.929
r_angle_other_deg	0.375
r_chiral_restr	0.043
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3591
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	236

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
XSCALE	data scaling
PHASER	phasing