2B5W | pdb_00002b5w

Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei

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	VAPOR DIFFUSION, HANGING DROP	7	290	pH 7.00, temperature 290K, Vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 290 KK

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.534	α = 90
b = 109.255	β = 90
c = 151.893	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	100	CCD	ADSC QUANTUM 4	MIRRORS	2002-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2		SRS	PX14.2

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	1.6	20	99.1	0.058	25.85	5.1		66155

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	1.6	1.64	98.2		0.543	2.69

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2B5V	1.6	20	62795	3356	98.8	0.154	0.17	0.186	0.2	RANDOM	21.16

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_scangle_it	16.687
r_scbond_it	14.42
r_mcangle_it	7.136
r_mcbond_it	5.986
r_dihedral_angle_1_deg	5.621
r_angle_refined_deg	1.555
r_angle_other_deg	0.854
r_symmetry_vdw_other	0.298
r_symmetry_hbond_refined	0.286
r_symmetry_vdw_refined	0.276
r_nbd_other	0.245
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.094
r_metal_ion_refined	0.092
r_nbtor_other	0.086
r_bond_refined_d	0.023
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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	2767
Nucleic Acid Atoms
Solvent Atoms	675
Heterogen Atoms	67

Software

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