1WLT

Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DZR	PDB ENTRY 1DZR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	15% PEG 3350, 0.1M Sodium cacodylate buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.147	α = 90
b = 73.145	β = 90
c = 126.242	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 4	MONOCHROMETER	2004-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0000	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.89	50	99.9	0.06	15.5	6.6	35811	35811		-3	24.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.89	1.96	99.7		0.379	6.43	6.3	3486

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DZR	1.9	20	33411	1759	99.98	0.19957	0.19705	0.2463	RANDOM	26.019

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]
0.87			-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.914
r_scangle_it	5.327
r_scbond_it	3.488
r_mcangle_it	2.312
r_angle_refined_deg	2.137
r_mcbond_it	1.392
r_angle_other_deg	1.011
r_symmetry_hbond_refined	0.31
r_symmetry_vdw_other	0.297
r_nbd_other	0.26
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.147
r_nbtor_other	0.094
r_bond_refined_d	0.03
r_gen_planes_other	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2915
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
SCALEPACK	data scaling
MOLREP	phasing