2VWQ

Haloferax mediterranei glucose dehydrogenase in complex with NADP and Zn.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B5V	PDB ENTRY 2B5V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		1.6M SODIUM CITRATE, 0.1M NAHEPES PH8.0, 10MM NADP

Crystal Properties
Matthews coefficient	Solvent content
3.2	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.884	α = 90
b = 111.113	β = 90
c = 152.227	γ = 90

Symmetry
Space Group	I 2 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	290	IMAGE PLATE	MARRESEARCH	MIRRORS	2001-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.1	30	90	0.07	22.7	3		33219

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	2.1	2.15	91.6		0.39	2.1	2.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2B5V	2.1	15	28810	1536	98	0.145	0.143	0.175	RANDOM	31.29

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]
0.66			0.69		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.605
r_dihedral_angle_4_deg	14.246
r_dihedral_angle_3_deg	12.573
r_scangle_it	7.676
r_mcangle_it	6.098
r_mcbond_it	5.729
r_scbond_it	5.53
r_dihedral_angle_1_deg	5.464
r_angle_refined_deg	1.277
r_angle_other_deg	0.893
r_xyhbond_nbd_refined	0.307
r_symmetry_vdw_other	0.267
r_nbd_refined	0.202
r_nbd_other	0.189
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.17
r_nbtor_other	0.084
r_chiral_restr	0.075
r_symmetry_hbond_refined	0.055
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2770
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing