3WFA

Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829812% (w/v) polyethylene glycol 6000, 0.1mM imidazole-HCl (pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5551.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.52α = 90
b = 111.96β = 100.49
c = 102.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2009-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
122095.80.0590.03414.93.91079582
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1191.50.1470.0877.83.815018

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 2d73219.812107892544095.70.1710.1710.2RANDOM14.9
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]
2.67-1.020.33-3
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.5
c_scangle_it2.12
c_scbond_it1.48
c_angle_deg1.4
c_mcangle_it1.26
c_mcbond_it0.87
c_improper_angle_d0.74
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11288
Nucleic Acid Atoms
Solvent Atoms1218
Heterogen Atoms42

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling