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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.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ACT PDB entry 2ACT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 PEG4000, Tris HCl, Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.9 34.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.2 α = 90 b = 58.76 β = 90 c = 69.35 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH osmic Max-Flux confocal optics 1999-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1 1.63 50 99.1 0.048 24.06 5.6 25294 25048 -3 18.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.67 89.2 0.281 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2ACT 1.63 14.94 25194 24993 1213 99.2 0.1626 0.161 0.161 0.1651 0.184 0.1902 RANDOM 17.8
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 Key Refinement Restraint Deviation c_dihedral_angle_d 23.8 c_scangle_it 4.74 c_scbond_it 3.11 c_mcangle_it 1.99 c_mcbond_it 1.31 c_angle_deg 1.2 c_improper_angle_d 0.74 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1632 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement