5V36 | pdb_00005v36

1.88 Angstrom Resolution Crystal Structure of Glutathione Reductase from Streptococcus mutans UA159 in Complex with FAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5U1O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 8.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1.mM FAD; Screen: Classics II (A5), 2M Ammonium sulfate, 0.1 HEPES (pH 7.5); Cryo: 4M Ammonium sulfate : 50% Sucrose (1:1)

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.333	α = 90
b = 126.333	β = 90
c = 247.876	γ = 120

Symmetry
Space Group	P 65 2 2

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	C(111)	2017-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	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	1.88	30	100	0.076	0.076	0.02	35.2	15.1		95700		-3	27.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91	99.7		0.775	0.775	0.21	0.888	3.8	14

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	5U1O	1.88	29.81	90417	4741	99.93	0.14424	0.14286	0.15	0.17048	0.18	RANDOM	29.111

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]
-0.32	-0.16		-0.32		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.838
r_dihedral_angle_4_deg	12.813
r_dihedral_angle_3_deg	10.103
r_long_range_B_refined	5.924
r_long_range_B_other	5.653
r_dihedral_angle_1_deg	3.865
r_scangle_other	2.756
r_scbond_it	1.838
r_scbond_other	1.837
r_mcangle_it	1.402
r_mcangle_other	1.402
r_angle_refined_deg	1.377
r_mcbond_it	0.94
r_mcbond_other	0.939
r_angle_other_deg	0.849
r_chiral_restr	0.083
r_gen_planes_refined	0.023
r_gen_planes_other	0.019
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6914
Nucleic Acid Atoms
Solvent Atoms	1034
Heterogen Atoms	329

Software

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