6JAM | pdb_00006jam

Crystal structure of ABC transporter alpha-glycoside-binding mutant protein R356A in complex with trehalose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6J9W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.4	277	0.04 M Citric Acid, 0.06 M Bis-Tris Propane, 16% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.07	α = 90
b = 85.07	β = 90
c = 146.38	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2018-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.63	73.55	100	0.078	0.082	0.026	0.999	22.1	18.3		67875

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	1.63	8.92	100		0.532	0.567	0.194	0.953	4.6	16.3

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6J9W	1.63	73.55	64378	3294	99.83	0.1395	0.1381	0.1659	0.174	RANDOM	19.422

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]
0.17			0.17		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.983
r_dihedral_angle_4_deg	16.697
r_dihedral_angle_3_deg	12.411
r_dihedral_angle_1_deg	5.642
r_angle_refined_deg	1.955
r_angle_other_deg	0.926
r_chiral_restr	0.12
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3236
Nucleic Acid Atoms
Solvent Atoms	587
Heterogen Atoms	62

Software

Software
Software Name	Purpose
HKL-3000	data collection
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction