7F6E | pdb_00007f6e

Crystal structure of metal-citrate-binding protein (MctA) of ABC transporter endogenously bound to Mg2+-citrate complex (Form I)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C9H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.5	293	0.1 M sodium citrate tribasic dihydrate pH 5.5, 16% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.27	α = 90
b = 144.25	β = 100.16
c = 79.15	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	2017-10-21	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	1.77	52.98	95.8	0.065	0.072	0.03	0.999	15.2	5.3		92348

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	1.77	1.8	88.9		0.411	0.458	0.198	0.879		5

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	3C9H	1.77	52.98	87826	4480	95.63	0.1385	0.1368	0.15	0.1715	0.18	RANDOM	23.425

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]
0.45		0.38	-0.22		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.29
r_dihedral_angle_4_deg	18.75
r_dihedral_angle_3_deg	13.137
r_dihedral_angle_1_deg	6.309
r_angle_refined_deg	1.811
r_angle_other_deg	1.555
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.29
r_dihedral_angle_4_deg	18.75
r_dihedral_angle_3_deg	13.137
r_dihedral_angle_1_deg	6.309
r_angle_refined_deg	1.811
r_angle_other_deg	1.555
r_chiral_restr	0.094
r_bond_refined_d	0.014
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	8016
Nucleic Acid Atoms
Solvent Atoms	716
Heterogen Atoms	179

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.