5JPD | pdb_00005jpd

Metal ABC transporter from Listeria monocytogenes with cadmium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HX7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.2 M magnesium chloride, 0.02 M cadmium chloride, 0.1 M Tris buffer, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.316	α = 90
b = 62.341	β = 90
c = 75.987	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	CCD	ADSC QUANTUM 210r		2016-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9792	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.72	28.3	98.4	0.093	16.5	5.1		29346

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.75	91		0.549	2.02	2.8

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	5HX7	1.72	28.2	27830	1460	98.34	0.1688	0.1669	0.1754	0.2071	0.2131	RANDOM	25.245

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]
1.2			-1.35		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.842
r_dihedral_angle_4_deg	14.545
r_dihedral_angle_3_deg	13.44
r_dihedral_angle_1_deg	5.992
r_mcangle_it	1.773
r_angle_refined_deg	1.291
r_mcbond_it	1.092
r_mcbond_other	1.087
r_angle_other_deg	0.759
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2204
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	14

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing