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


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_improper_angle_d 0.96
c_dihedral_angle_d 22.9
c_angle_deg 1.5
c_bond_d 0.009
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

Computing
Computing Package Purpose
XTALVIEW Structure Refinement
Software
Software Name Purpose
XTALVIEW refinement
CNS model building