5U9C

1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	Protein: 7.2 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (C5), 0.96M Sodium citrate (pH 7.0); Cryo: Screen : 50% Sucrose (1:1)

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.445	α = 90
b = 184.871	β = 90
c = 187.017	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	MARMOSAIC 225 mm CCD	C(111)	2014-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	30	99.6	0.07	0.07	28.8	7.5		179762		-3	28.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	96.3		0.649	0.887	2.7	6.8

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	SAD	THROUGHOUT	1.9	29.94	169660	8981	99.57	0.16146	0.15993	0.19066	RANDOM	40.524

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]
-2.11			4.39		-2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.252
r_dihedral_angle_4_deg	14.654
r_dihedral_angle_3_deg	8.865
r_long_range_B_refined	6.606
r_long_range_B_other	6.337
r_scangle_other	3.3
r_dihedral_angle_1_deg	2.94
r_mcangle_other	2.234
r_mcangle_it	2.233
r_scbond_it	2.112
r_scbond_other	2.103
r_angle_refined_deg	1.474
r_mcbond_it	1.403
r_mcbond_other	1.399
r_angle_other_deg	0.875
r_chiral_restr	0.102
r_gen_planes_refined	0.023
r_gen_planes_other	0.019
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13282
Nucleic Acid Atoms
Solvent Atoms	1446
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing