9S6C | pdb_00009s6c

B12 Binding protein - BtuK1

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	6.5	294.15	2mM Lanthanides, 0.1M Buffer systems 4 (MOPSO, Bis-Tris) (pH 6.5), 32.5% v/v Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6 Hexanetriol)

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.739	α = 90
b = 129.984	β = 90
c = 164.66	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 9M		2025-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

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	1.65	46.85	96.2	1	11.4	1		131196

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	1.65	1.71			0.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.817	14.287	99154	4991	96.307	0.164	0.1625	0.1643	0.1917	0.1954	34.173

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]
0.527			-0.598		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.9
r_dihedral_angle_other_2_deg	12.241
r_dihedral_angle_3_deg	11.669
r_dihedral_angle_1_deg	8.362
r_dihedral_angle_2_deg	8.173
r_lrange_it	5.779
r_lrange_other	5.638
r_scangle_it	3.933
r_scangle_other	3.932
r_scbond_it	2.536
r_scbond_other	2.534
r_angle_refined_deg	2.15
r_mcangle_it	2.107
r_mcangle_other	2.107
r_mcbond_it	1.552
r_mcbond_other	1.55
r_angle_other_deg	1.386
r_nbtor_refined	0.15
r_nbd_refined	0.138
r_chiral_restr	0.123
r_symmetry_nbd_refined	0.114
r_symmetry_nbd_other	0.112
r_nbd_other	0.112
r_symmetry_xyhbond_nbd_refined	0.111
r_xyhbond_nbd_refined	0.109
r_ncsr_local_group_1	0.083
r_ncsr_local_group_3	0.08
r_ncsr_local_group_2	0.077
r_symmetry_nbtor_other	0.058
r_gen_planes_refined	0.014
r_bond_refined_d	0.012
r_bond_other_d	0.009
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7939
Nucleic Acid Atoms
Solvent Atoms	642
Heterogen Atoms	279

Software

Software
Software Name	Purpose
Aimless	data scaling
gemmi	data extraction
REFMAC	refinement
autoPROC	data reduction
PHASER	phasing