☰ Navigation Tabs
Structure of a beta-1,4-mannanase, SsGH134.
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 Na HEPES, pH7.0
Crystal Properties Matthews coefficient Solvent content 2.24 45.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.91 α = 90 b = 53.68 β = 90 c = 81.45 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 2016-01-21 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) 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 1.09 33.62 99.9 0.066 12.2 6.1 68246 1.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.12 99.9 0.864 0.532 1.8 5.8
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 FREE R-VALUE alpha-helical fragment 1.09 33.62 64732 3439 99.77 0.14039 0.13913 0.16316 0.1439 RANDOM 14.314
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] 0.95 -0.48 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.306 r_sphericity_free 25.882 r_dihedral_angle_4_deg 20.366 r_dihedral_angle_3_deg 10.559 r_sphericity_bonded 9.236 r_dihedral_angle_1_deg 4.932 r_long_range_B_refined 3.018 r_long_range_B_other 3.017 r_rigid_bond_restr 2.073 r_scangle_other 1.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.306 r_sphericity_free 25.882 r_dihedral_angle_4_deg 20.366 r_dihedral_angle_3_deg 10.559 r_sphericity_bonded 9.236 r_dihedral_angle_1_deg 4.932 r_long_range_B_refined 3.018 r_long_range_B_other 3.017 r_rigid_bond_restr 2.073 r_scangle_other 1.996 r_mcangle_it 1.788 r_mcangle_other 1.787 r_scbond_it 1.639 r_scbond_other 1.638 r_angle_refined_deg 1.559 r_mcbond_other 1.354 r_mcbond_it 1.351 r_angle_other_deg 1.038 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 1212 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling ACORN phasing