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Crystal structure of beta-mannanase from a symbiotic protist of the termite Reticulitermes speratus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CBW PDB ENTRY 3CBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% PEG3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.503 α = 90 b = 61.405 β = 92.74 c = 57.806 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 270 2012-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.3 50 99.9 0.068 34.6 7.3 77823 77766
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 99.7 0.48 2.3 6.8 3846
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3CBW 1.3 28.87 77766 73833 3908 99.82 0.14489 0.1439 0.1531 0.16364 0.1726 RANDOM 14.538
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.739 r_dihedral_angle_4_deg 12.513 r_dihedral_angle_3_deg 11.145 r_dihedral_angle_1_deg 5.891 r_angle_refined_deg 1.477 r_angle_other_deg 0.817 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.739 r_dihedral_angle_4_deg 12.513 r_dihedral_angle_3_deg 11.145 r_dihedral_angle_1_deg 5.891 r_angle_refined_deg 1.477 r_angle_other_deg 0.817 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 2631 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling