1IZ8

Re-refinement of the structure of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution


X-RAY DIFFRACTION Experimental Data & Validation


Re-refined structure

This entry 1IZ8 reflects an alternative modeling of the structural data in r1d07sf, In PDB entry 1IZ8 information in remark 200 series is based on the experiment described in pdb entry 1D07 original data determined by author: J.MAREK,J.VEVODOVA,I.SMATANOVA,Y.NAGATA,L.A.SVENSSON,J.NEWMAN,M.TAKAGI,J.DAMBORSKY

Re-refined PDB record

DB record details: 1D07 - 1D07 CONTAINS THE SAME PROTEIN COMPLEXED WITH 1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, DIFFERENT REFINEMENT MODEL


X-ray Experimental Help

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.23 α = 90
b = 71.72 β = 90
c = 73.32 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline

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
-- -- -- -- -- -- -- -- n/a -- -- 13.0

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
-- 2.0 17.94 -- 4.0 -- 14610 1210 79.0 -- -- 0.166 0.248 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 2.0 2.2 -- 264 3070 0.199 0.303 0.019 73.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 20.5
Anisotropic B[1][1] -0.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.94
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.5
c_bond_d 0.009
c_dihedral_angle_d 22.9
c_improper_angle_d 0.96
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2322
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 310

Software

Software
Software Name Purpose
CNS refinement
XTALVIEW refinement