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Structure of an inactive (E45Q) variant of a beta-1,4-mannanase, SsGH134, in complex with Man5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other alpha-helical fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The protein stock in the buffer of 20 mM sodium phosphate, pH7.2 and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20 % PEG6000, 0.15-0.2 M CaCl2, and 0.1 M NaHEPES, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.707 α = 90 b = 53.841 β = 90 c = 82.636 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 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 0.96 45.11 84.1 0.054 0.998 12.4 5.9 84396
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 0.96 0.98 29.2 0.52 1.1 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT alpha-helical fragment 0.96 45.11 80165 4166 83.79 0.1227 0.12173 0.14133 0.1225 RANDOM 9.503
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] -0.13 -0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.746 r_sphericity_free 26.134 r_dihedral_angle_4_deg 15.197 r_dihedral_angle_3_deg 10.388 r_sphericity_bonded 6.962 r_dihedral_angle_1_deg 4.993 r_long_range_B_refined 2.969 r_long_range_B_other 2.967 r_rigid_bond_restr 1.798 r_scangle_other 1.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.746 r_sphericity_free 26.134 r_dihedral_angle_4_deg 15.197 r_dihedral_angle_3_deg 10.388 r_sphericity_bonded 6.962 r_dihedral_angle_1_deg 4.993 r_long_range_B_refined 2.969 r_long_range_B_other 2.967 r_rigid_bond_restr 1.798 r_scangle_other 1.762 r_angle_refined_deg 1.668 r_mcangle_it 1.371 r_mcangle_other 1.371 r_scbond_it 1.352 r_scbond_other 1.349 r_angle_other_deg 1.008 r_mcbond_other 1.006 r_mcbond_it 1.005 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1236 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling ACORN phasing