1OFN

Purification, crystallisation and preliminary structural studies of dTDP-4-keto-6-deoxy-glucose-5-epimerase (EvaD) from Amycolatopsis orientalis; the fourth enzyme in the dTDP-L-epivancosamine biosynthetic pathway.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details 25%PEG4K, 100MM MGCL2, 100MM TRIS-HCL, PH8.0, SITTING DROP,, pH 8.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.57 α = 90
b = 72 β = 90
c = 57.1 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD TOROIDAL MIRROR 2001-11-15
Diffraction Radiation
Monochromator Protocol
DIAMOND MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 -- ESRF ID14-2

Data Collection

Overall
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
1.5 57.74 100.0 0.056 -- -- 4.5 -- 65259 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.5 1.55 100.0 0.263 -- 2.6 4.1 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.5 57.74 -- -- -- 62417 3334 100.0 -- 0.146 0.144 0.178 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.5 1.54 -- 239 4533 0.171 0.22 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.21
Anisotropic B[1][1] -0.49
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.943
r_nbd_refined 0.226
r_symmetry_vdw_other 0.256
r_scangle_it 4.947
r_mcbond_it 1.446
r_symmetry_vdw_refined 0.44
r_xyhbond_nbd_other 0.176
r_angle_other_deg 0.754
r_bond_refined_d 0.018
r_gen_planes_other 0.008
r_gen_planes_refined 0.009
r_nbd_other 0.198
r_angle_refined_deg 1.71
r_symmetry_hbond_refined 0.402
r_dihedral_angle_1_deg 5.337
r_chiral_restr 0.1
r_mcangle_it 2.231
r_bond_other_d 0.001
r_scbond_it 3.243
r_xyhbond_nbd_refined 0.192
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3123
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 543

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
MOSFLM data reduction
SCALEPACK data scaling
AMoRE phasing