3DBN

Crystal structure of the Streptoccocus suis serotype2 D-mannonate dehydratase in complex with its substrate

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.52	α = 90
b = 105.52	β = 90
c = 160.077	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		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	2.9	88.04					20245

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	2.9	50	18872	981	95.8	0.23373	0.23132	0.28031	RANDOM	22.971

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]
-0.69			-0.69		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.207
r_dihedral_angle_4_deg	20.907
r_dihedral_angle_3_deg	20.007
r_dihedral_angle_1_deg	7.306
r_scangle_it	1.873
r_angle_refined_deg	1.579
r_scbond_it	1.16
r_mcangle_it	0.951
r_mcbond_it	0.523
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.263
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.224
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.107
r_bond_refined_d	0.013
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_refined
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	5469
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement