8BAZ | pdb_00008baz

The surface-exposed lipo-protein of BtuG2 in complex with cyanocobalamin.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	50 mM TRIS pH, 100 mM NaCl, 20 mM ZnCl, 20 mM Cyanocobalamin, PEG2000 20%

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.177	α = 90
b = 100.593	β = 97.6
c = 79.579	γ = 90

Symmetry
Space Group	P 1 21 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		2021-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1	ESRF	ID23-1

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	78.89	99	0.96	14	8		51840

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	8			0.94

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6FFV	2	44.199	51786	2531	99.896	0.184	0.181	0.19	0.2432	0.25	RANDOM	29.056

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]
4.305		1.984	-3.026		-1.747

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.588
r_dihedral_angle_3_deg	14.227
r_dihedral_angle_2_deg	12.888
r_dihedral_angle_1_deg	7.763
r_rigid_bond_restr	3.988
r_lrange_it	3.824
r_lrange_other	3.823
r_scangle_it	2.817
r_scangle_other	2.817
r_mcangle_it	2.46
r_mcangle_other	2.46
r_scbond_it	2.068
r_scbond_other	2.068
r_angle_refined_deg	1.806
r_mcbond_it	1.703
r_mcbond_other	1.689
r_angle_other_deg	0.778
r_nbd_other	0.261
r_symmetry_nbd_refined	0.239
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.174
r_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.149
r_chiral_restr	0.135
r_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.081
r_ncsr_local_group_1	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5247
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	331

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing