7CGZ

glucose dehydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CDY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.622	α = 90
b = 44.64	β = 100.096
c = 99.885	γ = 90

Symmetry
Space Group	C 1 2 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	PIXEL	DECTRIS PILATUS 6M		2017-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.977	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.94	20	97.8	0.04	25.87	6.4		50863

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.97			0.223	0.914	2.28

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7cdy	1.94	20	50863	2545	96.397	0.205	0.203	0.2347	37.697

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]
-4.103		-0.46	6.089		-1.713

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.356
r_dihedral_angle_4_deg	16.714
r_dihedral_angle_3_deg	14.419
r_dihedral_angle_1_deg	6.918
r_lrange_other	5.234
r_lrange_it	5.233
r_scangle_it	4.463
r_scangle_other	4.462
r_scbond_it	4.105
r_scbond_other	4.104
r_mcangle_it	3.515
r_mcangle_other	3.515
r_mcbond_it	2.766
r_mcbond_other	2.766
r_angle_other_deg	2.275
r_angle_refined_deg	1.718
r_symmetry_xyhbond_nbd_refined	0.363
r_nbd_other	0.238
r_symmetry_nbd_other	0.231
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.17
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.096
r_metal_ion_refined	0.083
r_symmetry_xyhbond_nbd_other	0.071
r_bond_other_d	0.035
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5151
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	8

Software

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