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Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 1 M ammonium citrate, 15%(v/v) iso-propanol, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.91 30.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.13 α = 90 b = 69.461 β = 90 c = 86.654 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 PILATUS3 S 6M 2015-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.7 55 98.4 0.088 0.998 13.1 3.4 33115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.81 97.1 0.554 0.825 2.7 3.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C0H 1.7 54.2 31789 1711 98.97 0.13238 0.13036 0.1333 0.16927 0.1699 RANDOM 23.891
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] 0.03 -0.79 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.406 r_dihedral_angle_4_deg 22.852 r_dihedral_angle_3_deg 11.797 r_dihedral_angle_1_deg 7.514 r_long_range_B_refined 4.602 r_long_range_B_other 4.464 r_scangle_other 3.351 r_scbond_it 2.349 r_scbond_other 2.348 r_mcangle_it 2.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.406 r_dihedral_angle_4_deg 22.852 r_dihedral_angle_3_deg 11.797 r_dihedral_angle_1_deg 7.514 r_long_range_B_refined 4.602 r_long_range_B_other 4.464 r_scangle_other 3.351 r_scbond_it 2.349 r_scbond_other 2.348 r_mcangle_it 2.323 r_mcangle_other 2.323 r_angle_refined_deg 1.903 r_mcbond_it 1.724 r_mcbond_other 1.724 r_angle_other_deg 1.008 r_chiral_restr 0.141 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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 2784 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing