8C33 | pdb_00008c33

Anaerobic light exposed 2.25 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8C31

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Condition B3 from Morpheus screen (Molecular Dimensions) (0.09 M halogens, 0.1 M buffer system 1 pH 6.5, 30% v/v precipitant mix 3 dark adapted crystals were exposed to light under anaerobic conditions inside a glove box for 30-40 secs

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.918	α = 90
b = 72.622	β = 90
c = 200.943	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 EIGER2 X 16M		2021-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9765	Diamond	I04

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	2.25	60.92	100	1	9.4	13.4		43294

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	2.25	2.29	98.4		0.7	1.2	13.3

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	THROUGHOUT	8C31	2.25	58.93	41071	2147	99.91	0.20009	0.19758	0.2	0.24798	0.26	RANDOM	39.485

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]
0.25			-1.83		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.14
r_dihedral_angle_2_deg	8.069
r_dihedral_angle_1_deg	5.737
r_long_range_B_refined	5.586
r_long_range_B_other	5.562
r_scangle_other	4.105
r_mcangle_it	2.688
r_mcangle_other	2.688
r_scbond_it	2.527
r_scbond_other	2.526
r_angle_refined_deg	1.867
r_mcbond_it	1.736
r_mcbond_other	1.736
r_angle_other_deg	0.488
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6003
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	365

Software

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