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Crystal structure of Cucumisin complex with pro-peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium Sulfate,
Pentaerythritol Ethoxylate
Crystal Properties Matthews coefficient Solvent content 2.49 50.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.738 α = 90 b = 97.738 β = 90 c = 73.433 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2013-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.95 50 98.5 0.095 19.5 7.3 49147 25.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 97.8 0.686 3.7 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3VTA 1.95 34.56 49146 2468 98.2 0.184 0.184 0.1948 0.222 0.2326 RANDOM 41.3
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] 1.94 1.94 -3.88
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 2.72 c_mcangle_it 2.04 c_scbond_it 1.86 c_mcbond_it 1.34 c_angle_deg 1.3 c_improper_angle_d 0.79 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.4 c_scangle_it 2.72 c_mcangle_it 2.04 c_scbond_it 1.86 c_mcbond_it 1.34 c_angle_deg 1.3 c_improper_angle_d 0.79 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5047 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 98
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing