8OVV | pdb_00008ovv

Tagless BtuM in complex with hydroxycobalamin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Potassium chloride, 0.1 M Sodium citrate pH 5.5, 37 % v/v Pentaerythritol propoxylate (PO/OH).

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.982	α = 90
b = 95.982	β = 90
c = 77.291	γ = 120

Symmetry
Space Group	P 32 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 PILATUS 6M		2021-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.98435	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.9	83.123	75.6	0.066	0.093	0.066	0.991	15.5	1.9		17803			27.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	1.7		1.013	1.433	1.013	0.291	0.3	1.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.26	83.123	15825	782	80.592	0.183	0.1816	0.16	0.202	0.18	36.694

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]
-20.249			-20.249		40.498

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.141
r_dihedral_angle_3_deg	15.56
r_dihedral_angle_2_deg	12.629
r_rigid_bond_restr	9.228
r_lrange_it	7.927
r_scangle_it	6.068
r_dihedral_angle_1_deg	5.801
r_mcangle_it	4.931
r_scbond_it	4.468
r_mcbond_it	3.273
r_angle_refined_deg	1.738
r_nbtor_refined	0.323
r_nbd_refined	0.234
r_symmetry_nbd_refined	0.214
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1348
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	196

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building