3CXR

Crystal structure of gluconate 5-dehydrogase from streptococcus suis type 2

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.147	α = 90
b = 75.378	β = 90
c = 97.674	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		IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

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

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	1.9	59.66					19757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	30.56			4.2		19757

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1vl8	2	30.56	16716	888	97.06	0.21	0.19193	0.19111	0.20772	RANDOM	22.88

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]
-1.2			0.33		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.824
r_dihedral_angle_4_deg	15.257
r_dihedral_angle_3_deg	14.238
r_dihedral_angle_1_deg	5.533
r_scangle_it	3.026
r_scbond_it	2.077
r_angle_refined_deg	1.243
r_mcangle_it	1.182
r_mcbond_it	0.724
r_nbtor_refined	0.304
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.103
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1938
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing