4MB5

Crystal structure of E153Q mutant of cold-adapted chitinase from Moritella complex with Nag5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HMC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529212.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02M Na-L-glutamate, 0.02M alanine (racemic), 0.02M glycine, 0.02M lysine HCl (racemic), 0.02M serine (racemic), 0.1M MES/imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.8456.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.057α = 90
b = 67.057β = 90
c = 256.633γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.63934.4499.90.07217.726.58164281642-316.83
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6391.7499.30.9051.896.52

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT4HMC1.63934.43928164281625100099.860.14670.14630.17724.5852
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.291
f_angle_d1.769
f_chiral_restr0.215
f_bond_d0.019
f_plane_restr0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4137
Nucleic Acid Atoms
Solvent Atoms700
Heterogen Atoms119

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing