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 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_bond_other_d 0.001
r_scangle_it 4.947
r_gen_planes_other 0.008
r_symmetry_vdw_other 0.256
r_dihedral_angle_3_deg 16.943
r_angle_refined_deg 1.71
r_bond_refined_d 0.018
r_chiral_restr 0.1
r_mcbond_it 1.446
r_xyhbond_nbd_other 0.176
r_symmetry_vdw_refined 0.44
r_nbd_refined 0.226
r_gen_planes_refined 0.009
r_xyhbond_nbd_refined 0.192
r_angle_other_deg 0.754
r_symmetry_hbond_refined 0.402
r_mcangle_it 2.231
r_dihedral_angle_1_deg 5.337
r_nbd_other 0.198
r_scbond_it 3.243
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
AMORE model building
REFMAC version: 5.0 refinement