8OKV | pdb_00008okv

lipoprotein BT2095 from Bacteroides thetaiotamicron bound to cyanocobalamin CnCbl

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Optimised from Index H8, 0.1MgFormate 15% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.77	α = 90
b = 131.04	β = 90
c = 179.38	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 XE 16M		2021-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9794	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim 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	2.6	74.7	99.4	0.06	0.99	11.8	13.2		54678

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	2.6	2.68			0.66	1.1

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	2.6	74.123	54607	2675	99.253	0.221	0.2182	0.23	0.276	0.28	71.314

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]
-3.316			4.184		-0.868

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.463
r_dihedral_angle_6_deg	15.96
r_dihedral_angle_2_deg	13.158
r_lrange_it	10.071
r_lrange_other	10.071
r_dihedral_angle_1_deg	9.311
r_scangle_it	8.54
r_scangle_other	8.539
r_mcangle_it	7.744
r_mcangle_other	7.744
r_scbond_it	5.969
r_scbond_other	5.969
r_mcbond_it	5.535
r_mcbond_other	5.534
r_angle_refined_deg	2.466
r_angle_other_deg	0.896
r_xyhbond_nbd_refined	0.192
r_symmetry_nbd_refined	0.183
r_nbd_other	0.177
r_nbd_refined	0.174
r_nbtor_refined	0.17
r_symmetry_nbd_other	0.166
r_symmetry_xyhbond_nbd_refined	0.154
r_chiral_restr	0.132
r_ncsr_local_group_3	0.117
r_ncsr_local_group_2	0.116
r_ncsr_local_group_1	0.111
r_ncsr_local_group_6	0.108
r_ncsr_local_group_4	0.106
r_ncsr_local_group_5	0.094
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.014
r_symmetry_xyhbond_nbd_other	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10619
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	372

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data scaling
PHASER	phasing