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The structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManMIm
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 100MM SODIUM CITRATE PH 5.6, 15% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.81 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.507 α = 90 b = 84.507 β = 90 c = 244.941 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 2012-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.1 32 100 0.1 11.7 15.3 208589 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.12 100 1 10
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 1.1 73.19 197844 10555 99.98 0.15273 0.15171 0.1628 0.17213 0.1824 RANDOM 14.118
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] -0.36 -0.18 -0.36 1.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.761 r_dihedral_angle_2_deg 33.231 r_rigid_bond_restr 19.642 r_dihedral_angle_4_deg 15.365 r_sphericity_bonded 12.176 r_dihedral_angle_3_deg 11.447 r_dihedral_angle_1_deg 5.919 r_scangle_it 3.207 r_scbond_it 2.657 r_mcangle_it 2.217
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.761 r_dihedral_angle_2_deg 33.231 r_rigid_bond_restr 19.642 r_dihedral_angle_4_deg 15.365 r_sphericity_bonded 12.176 r_dihedral_angle_3_deg 11.447 r_dihedral_angle_1_deg 5.919 r_scangle_it 3.207 r_scbond_it 2.657 r_mcangle_it 2.217 r_mcbond_other 1.918 r_mcbond_it 1.917 r_angle_refined_deg 1.549 r_angle_other_deg 0.916 r_nbd_refined 0.259 r_symmetry_vdw_refined 0.254 r_symmetry_vdw_other 0.203 r_nbtor_refined 0.185 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.127 r_metal_ion_refined 0.107 r_chiral_restr 0.103 r_symmetry_hbond_refined 0.082 r_nbtor_other 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_xyhbond_nbd_other 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 2935 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing