☰ Navigation Tabs
Recombinant stem bromelain precursor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 A reservoir solution comprised of 19% (w/v) PEG6000, 0.01 M Zinc chloride and 0.1 M MMT, pH4. Using an equal reservoir to protein (8 mg/ml) ratio, crystals were observed after 1 day and grew to maximal size after 2 week.
Crystal Properties Matthews coefficient Solvent content 2.26 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.31 α = 90 b = 69.94 β = 90 c = 74.25 γ = 90
Symmetry Space Group P 2 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 193 CCD ADSC QUANTUM 210r 2018-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953695 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3 47.38 100 0.07 0.265 0.095 0.992 10.7 14.2 7132
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 100 0.844 0.879 0.228 0.903 14.5
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 6OKJ 3 47.38 6766 323 99.8 0.2032 0.1982 0.2033 0.3138 0.307 RANDOM 25.22
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] 0.01 0.31 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.931 r_dihedral_angle_4_deg 21.019 r_dihedral_angle_3_deg 18.807 r_dihedral_angle_1_deg 8.738 r_angle_refined_deg 1.62 r_angle_other_deg 1.244 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.931 r_dihedral_angle_4_deg 21.019 r_dihedral_angle_3_deg 18.807 r_dihedral_angle_1_deg 8.738 r_angle_refined_deg 1.62 r_angle_other_deg 1.244 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2335 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling PHENIX phasing