1IWD

Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ACTPDB entry 2ACT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5292PEG4000, Tris HCl, Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.934.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.2α = 90
b = 58.76β = 90
c = 69.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHosmic Max-Flux confocal optics1999-03-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54

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
11.635099.10.04824.065.62529425048-318.1
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)
11.631.6789.20.2814

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2ACT1.6314.942519424993121399.20.16260.1610.1610.184RANDOM17.8
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]
1.72-1.07-0.65
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it4.74
c_scbond_it3.11
c_mcangle_it1.99
c_mcbond_it1.31
c_angle_deg1.2
c_improper_angle_d0.74
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1632
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms5

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement