3ENN

2.1A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis (p43212)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	289	45% MPD, 0.1M TRIS pH 8.5, 0.2M AMMONIUM ACETATE, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.5	α = 90
b = 119.5	β = 90
c = 136	γ = 90

Symmetry
Space Group	P 43 21 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	SATURN 944	MULTI-LAYER OPTICS MIRRORS	2008-09-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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		99.8	0.1				57871		-3	31.3

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)
	2.1	2.15	100		0.481	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.1		57869	2938	99.81	0.19	0.188	0.23	RANDOM	24.884

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]
-0.29			-0.29		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_4_deg	19.497
r_dihedral_angle_3_deg	17.508
r_dihedral_angle_1_deg	5.595
r_scangle_it	3.038
r_scbond_it	1.862
r_angle_refined_deg	1.369
r_mcangle_it	1.184
r_mcbond_it	0.693
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_4_deg	19.497
r_dihedral_angle_3_deg	17.508
r_dihedral_angle_1_deg	5.595
r_scangle_it	3.038
r_scbond_it	1.862
r_angle_refined_deg	1.369
r_mcangle_it	1.184
r_mcbond_it	0.693
r_nbtor_refined	0.306
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.192
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7066
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.