7C1B | pdb_00007c1b

Crystal structure of a dinucleotide-binding protein (F79A/Y224A/Y246A and deletion of residues 50-75) of ABC transporter (unbound form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C0F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	277	0.2M ammonium sulphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.93	α = 90
b = 55.47	β = 90
c = 124.4	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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2019-12-08	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	2.3	62.2	100	0.15	0.157	0.048	0.997	11.5	10.7		16950

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	2.3	2.38	100		0.559	0.586	0.177	0.928		10.8

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7C0F	2.3	62.2	16069	829	99.99	0.1986	0.195	0.2	0.2695	0.27	RANDOM	30.045

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]
2.08			-1.77		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.427
r_dihedral_angle_4_deg	22.045
r_dihedral_angle_3_deg	19.85
r_dihedral_angle_1_deg	6.832
r_angle_refined_deg	1.821
r_angle_other_deg	1.37
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.427
r_dihedral_angle_4_deg	22.045
r_dihedral_angle_3_deg	19.85
r_dihedral_angle_1_deg	6.832
r_angle_refined_deg	1.821
r_angle_other_deg	1.37
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2817
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	11

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.