4GNR | pdb_00004gnr

1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Z18

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Protein at 66 mg/mL, Crystallization condition: PEG 4K 30% w/v Mg Chloride 0.2M Tris0.1M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.274	α = 90
b = 72.819	β = 105.1
c = 57.542	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	CCD	MARMOSAIC 300 mm CCD	Be-Lenses	2012-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	30	99.7	0.048	22.85	4.5	159549	159549		-3	7

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	1.02	98		0.487	2.2	3	7818

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1z18	1	27.78	151086	151086	7976	99.69	0.12722	0.12622	0.13	0.14656	0.15	RANDOM	9.151

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]
0.07		-0.1	0.09		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.509
r_dihedral_angle_3_deg	8.186
r_dihedral_angle_4_deg	6.454
r_scangle_it	4.383
r_dihedral_angle_1_deg	3.47
r_scbond_it	2.917
r_mcbond_other	2.572
r_mcangle_it	2.105
r_angle_refined_deg	1.747
r_mcbond_it	1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.509
r_dihedral_angle_3_deg	8.186
r_dihedral_angle_4_deg	6.454
r_scangle_it	4.383
r_dihedral_angle_1_deg	3.47
r_scbond_it	2.917
r_mcbond_other	2.572
r_mcangle_it	2.105
r_angle_refined_deg	1.747
r_mcbond_it	1.41
r_rigid_bond_restr	1.317
r_angle_other_deg	1.084
r_chiral_restr	0.108
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2582
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms	14

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.