8BFY | pdb_00008bfy

ABC transporter binding protein CebE from Streptomyces scabiei in complex with cellotriose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		alphafold model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3.5	277	PEG3350 25%, sodium citrate pH 3.5 100mM

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.39	α = 90
b = 39.43	β = 92.38
c = 79.64	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 PILATUS3 6M		2014-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.55	35.33	99.2	0.084	0.999	13.15	3.8		53542

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	97.1		1.333	0.524		3.14

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	alphafold model	1.55	35.33	53542	2678	99.227	0.138	0.1357	0.14	0.1776	0.18	24.808

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]
-0.762		-0.407	-0.977		1.766

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.218
r_dihedral_angle_3_deg	14.021
r_dihedral_angle_2_deg	11.125
r_dihedral_angle_1_deg	6.358
r_lrange_it	3.15
r_rigid_bond_restr	3.133
r_lrange_other	2.742
r_scangle_it	1.969
r_scangle_other	1.969
r_mcangle_it	1.712
r_mcangle_other	1.712
r_scbond_it	1.452
r_scbond_other	1.451
r_angle_refined_deg	1.373
r_mcbond_it	1.251
r_mcbond_other	1.23
r_angle_other_deg	0.458
r_symmetry_xyhbond_nbd_refined	0.239
r_nbd_refined	0.221
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.15
r_nbd_other	0.14
r_symmetry_nbd_refined	0.132
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2974
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	65

Software

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