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The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManIFG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX7 PDB ENTRY 2VX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 100 MM SODIUM CITRATE PH 5.6, 15% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.518 α = 90 b = 84.518 β = 90 c = 244.491 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.2 54.46 88.8 0.06 21.9 14.8 142150 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 20.8 0.69 0.8 1.4
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 2VX7 1.2 73.19 134854 7145 88.73 0.11241 0.11129 0.1263 0.13385 0.1459 RANDOM 15.02
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 0.01 0.03 -0.08
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.159 r_dihedral_angle_2_deg 33.127 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 11.237 r_sphericity_bonded 8.371 r_dihedral_angle_1_deg 5.88 r_rigid_bond_restr 2.391 r_scangle_it 1.768 r_angle_refined_deg 1.519 r_scbond_it 1.51
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.159 r_dihedral_angle_2_deg 33.127 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 11.237 r_sphericity_bonded 8.371 r_dihedral_angle_1_deg 5.88 r_rigid_bond_restr 2.391 r_scangle_it 1.768 r_angle_refined_deg 1.519 r_scbond_it 1.51 r_angle_other_deg 1.285 r_mcangle_it 1.228 r_mcbond_it 0.99 r_mcbond_other 0.989 r_symmetry_vdw_refined 0.379 r_nbd_refined 0.272 r_symmetry_vdw_other 0.247 r_nbd_other 0.196 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.138 r_metal_ion_refined 0.126 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.083 r_nbtor_other 0.079 r_xyhbond_nbd_other 0.014 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2933 Nucleic Acid Atoms Solvent Atoms 746 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing