8GRJ | pdb_00008grj

Crystal structure of gamma-alpha subunit complex from Burkholderia cepacia FAD glucose dehydrogenase in complex with gluconolactone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6A2U	6A2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Tacsimate

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.235	α = 90
b = 111.235	β = 90
c = 527.106	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	ADSC QUANTUM 315		2013-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

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	2.95	100	99.4	0.113	7.4	15.5		42134

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	2.95	3	100		0.424		16.3

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	6A2U	2.95	50.04	39931	2125	99.51	0.2018	0.1982	0.2021	0.2702	0.2699	RANDOM	37.59

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]
					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.925
r_dihedral_angle_3_deg	22.209
r_dihedral_angle_4_deg	21.338
r_dihedral_angle_1_deg	7.87
r_angle_refined_deg	1.705
r_angle_other_deg	1.187
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10032
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	144

Software

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