7F6P | pdb_00007f6p

Crystal structure of metal-citrate-binding mutant (D28A) protein (MctA) of ABC transporter endogenously bound to citrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7F6E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	0.2 M ammonium phosphate dibasic, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.31	α = 90
b = 146.26	β = 99.89
c = 79.09	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	IMAGE PLATE	RIGAKU RAXIS IV	VariMax HF	2019-12-29	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	2.15	73.24	95.5	0.091	0.1	0.041	0.997	12.7	5.5		52451

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	2.15	2.21	91.4		0.596	0.656	0.271	0.851		5.3

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7F6E	2.15	73.24	49852	2565	95.32	0.1757	0.1737	0.18	0.2144	0.22	RANDOM	52.468

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]
-0.51		0.14	1.72		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	17.338
r_dihedral_angle_3_deg	15.746
r_dihedral_angle_1_deg	6.76
r_angle_refined_deg	1.708
r_angle_other_deg	1.42
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.942
r_dihedral_angle_4_deg	17.338
r_dihedral_angle_3_deg	15.746
r_dihedral_angle_1_deg	6.76
r_angle_refined_deg	1.708
r_angle_other_deg	1.42
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7935
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms	68

Software

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