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The structure of the M60 catalytic domain with the CBM51-1 and CBM51-2 domains from Clostridium perfringens ZmpB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KDN PDB entry 5KDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 291 0.2 M potassium citrate tribasic monohydrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.908 α = 90 b = 119.321 β = 90 c = 129.68 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 100 PIXEL DECTRIS PILATUS 200K 2020-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.6 30 99.9 0.204 0.092 0.977 8.7 4.8 6474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.6 4.68 100 0.741 0.348 0.849 2.3 4.8
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 PDB entry 5KDN 4.6 29.69 6112 294 98.54 0.1945 0.1914 0.1926 0.2582 0.2176 RANDOM 84.268
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] -2.12 -0.62 2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.751 r_dihedral_angle_4_deg 16.689 r_dihedral_angle_3_deg 11.15 r_dihedral_angle_1_deg 5.643 r_angle_refined_deg 1.563 r_chiral_restr 0.095 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7510 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing