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Mannanase KMAN from Klebsiella oxytoca KUB-CW2-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 2.0 M Ammonium sulfate, 0.2 M Sodium chloride, 0.1 M Sodium cacodylate buffer (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 3.4 63.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.547 α = 90 b = 83.547 β = 90 c = 146.329 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX SX-165mm 2020-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLRI BEAMLINE BL7.2W 0.97900 SLRI BL7.2W
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 2.57 59.07 99.4 0.377 0.404 0.144 0.981 7.8 14.3 17034
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 2.57 2.69 1.313 1.413 0.517 0.709 13.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3cbw 2.57 55.04 16148 847 99.3 0.20228 0.19987 0.2491 0.2054 RANDOM 17.59
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] 0.31 0.31 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.73 r_dihedral_angle_3_deg 17.239 r_dihedral_angle_4_deg 15.398 r_dihedral_angle_1_deg 7.362 r_long_range_B_refined 3.541 r_long_range_B_other 3.422 r_scangle_other 2.223 r_mcangle_it 2.051 r_mcangle_other 2.05 r_angle_refined_deg 1.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.73 r_dihedral_angle_3_deg 17.239 r_dihedral_angle_4_deg 15.398 r_dihedral_angle_1_deg 7.362 r_long_range_B_refined 3.541 r_long_range_B_other 3.422 r_scangle_other 2.223 r_mcangle_it 2.051 r_mcangle_other 2.05 r_angle_refined_deg 1.599 r_scbond_it 1.391 r_scbond_other 1.365 r_angle_other_deg 1.282 r_mcbond_it 1.24 r_mcbond_other 1.205 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2608 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data reduction DIALS data reduction DIALS data scaling PHASER phasing