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Structure of apo structure of GH36 alpha-galactosidase from Thermotoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZY9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M magnesium sulfate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.96 α = 90 b = 95.78 β = 90 c = 97.54 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 80 PIXEL DECTRIS PILATUS 6M 2013-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
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 1.8 32.09 99 0.079 14.9 6.4 59066
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 1.8 1.85 99.2 0.706 2.6 6.4
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 1ZY9 1.8 32.09 55012 2938 97.09 0.18845 0.18613 0.1952 0.23128 0.2375 RANDOM 29.643
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] 4.74 -2.2 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.876 r_dihedral_angle_4_deg 15.395 r_dihedral_angle_3_deg 14.382 r_dihedral_angle_1_deg 6.61 r_long_range_B_refined 6.27 r_long_range_B_other 6.234 r_scangle_other 4.976 r_scbond_it 3.299 r_scbond_other 3.256 r_mcangle_it 3.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.876 r_dihedral_angle_4_deg 15.395 r_dihedral_angle_3_deg 14.382 r_dihedral_angle_1_deg 6.61 r_long_range_B_refined 6.27 r_long_range_B_other 6.234 r_scangle_other 4.976 r_scbond_it 3.299 r_scbond_other 3.256 r_mcangle_it 3.163 r_mcangle_other 3.162 r_mcbond_it 2.314 r_mcbond_other 2.307 r_angle_refined_deg 1.795 r_angle_other_deg 1.014 r_chiral_restr 0.111 r_bond_refined_d 0.017 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4311 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction XDS data scaling MOLREP phasing Coot model building