2D20

Crystal structure of michaelis complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D1ZPDB ENTRY 2D1Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293disodium hydrogenphosphate, citric acid, ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7597155.430107

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.472α = 90
b = 94.111β = 90
c = 139.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102004-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.978Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85501001703098875714.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.92100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2D1Z1.8544.61066678866244720.1810.1810.208RANDOM20.6
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]
-0.05-0.020.07
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_angle_deg1.3
c_improper_angle_d0.7
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6466
Nucleic Acid Atoms
Solvent Atoms825
Heterogen Atoms99

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing