4YNU | pdb_00004ynu

Crystal structure of Aspergillus flavus FADGDH in complex with D-glucono-1,5-lactone

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CF3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M BisTris, 20-25 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.658	α = 90
b = 64.877	β = 100.46
c = 75.889	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	ADSC QUANTUM 315r		2014-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	1.57	50	99.9	0.059	10.6	3.7		65992

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	1.57	1.6	97.6		0.48		3	3221

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	1CF3	1.57	39.02	62625	3347	99.73	0.1419	0.1407	0.15	0.1642	0.17	RANDOM	20.571

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.56
r_dihedral_angle_4_deg	21.04
r_dihedral_angle_3_deg	14.18
r_dihedral_angle_1_deg	7.316
r_angle_refined_deg	1.123
r_angle_other_deg	0.642
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.56
r_dihedral_angle_4_deg	21.04
r_dihedral_angle_3_deg	14.18
r_dihedral_angle_1_deg	7.316
r_angle_refined_deg	1.123
r_angle_other_deg	0.642
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4324
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	phasing

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.