3A9G

Crystal Structure of PQQ-dependent sugar dehydrogenase apo-form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop	6.6	293	ammonium sulfate, pH 6.6, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.76	74.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.74	α = 90
b = 177.74	β = 90
c = 89.937	γ = 90

Symmetry
Space Group	I 41 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 270		2009-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.39	50	99.9			28570	28570

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2ISM	2.39	40.13	28369	27108	1448	99.62	0.20167	0.20068	0.21989	RANDOM	38.722

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]
-3.31			-3.31		6.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.904
r_dihedral_angle_4_deg	21.033
r_dihedral_angle_3_deg	18.439
r_dihedral_angle_1_deg	6.828
r_scangle_it	2.747
r_scbond_it	1.776
r_angle_refined_deg	1.519
r_mcangle_it	1.494
r_mcbond_it	0.832
r_nbtor_refined	0.311
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.109
r_chiral_restr	0.104
r_metal_ion_refined	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2571
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	47

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement