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Native structure of endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.8 M phosphate, 0.2 M sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.463 α = 90 b = 83.352 β = 90 c = 92.179 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 CCD MARMOSAIC 225 mm CCD 2010-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.42 40.33 98.4 80074 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 1.42 1.47 86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SIRAS THROUGHOUT 1.42 40.33 79961 79961 4002 98.34 0.14714 0.14545 0.17849 0.1731 RANDOM 17.845
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] 0.15 -0.45 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.34 r_sphericity_free 14.313 r_dihedral_angle_4_deg 13.777 r_dihedral_angle_3_deg 12.461 r_sphericity_bonded 8.425 r_scangle_it 6.321 r_dihedral_angle_1_deg 6.094 r_scbond_it 4.787 r_mcangle_it 3.72 r_rigid_bond_restr 3.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.34 r_sphericity_free 14.313 r_dihedral_angle_4_deg 13.777 r_dihedral_angle_3_deg 12.461 r_sphericity_bonded 8.425 r_scangle_it 6.321 r_dihedral_angle_1_deg 6.094 r_scbond_it 4.787 r_mcangle_it 3.72 r_rigid_bond_restr 3.011 r_mcbond_it 2.747 r_angle_refined_deg 2.229 r_chiral_restr 0.175 r_bond_refined_d 0.03 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2927 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection SHELX model building REFMAC refinement DENZO data reduction SCALEPACK data scaling SHELX phasing