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The Crystal Structure of Chrysonilia sitophila endo-beta-D-1,4- mannanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QNO PDB ENTRY 1QNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M MAGNESIUM CHLORIDE, 0.1M BIS-TRIS PH 5.5, 25% (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.22 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.36 α = 90 b = 78.94 β = 90 c = 83.86 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 PILATUS 6M LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR AND A CYLINDRICAL GRAZING INCIDENCE MIRROR 2011-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.4 41.93 99.5 0.12 6.5 4.6 75187 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 1.4 1.44 96 0.39 2.2 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 1QNO 1.4 41.93 71225 3772 99.2 0.16257 0.16053 0.1575 0.20215 0.1972 RANDOM 15.804
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] 0.44 -1.46 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.894 r_dihedral_angle_4_deg 14.886 r_sphericity_free 14.76 r_dihedral_angle_3_deg 11.31 r_sphericity_bonded 8.017 r_dihedral_angle_1_deg 5.841 r_angle_refined_deg 1.237 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.894 r_dihedral_angle_4_deg 14.886 r_sphericity_free 14.76 r_dihedral_angle_3_deg 11.31 r_sphericity_bonded 8.017 r_dihedral_angle_1_deg 5.841 r_angle_refined_deg 1.237 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3046 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing