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Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 20% PEG MME 2000, 100 mM HEPES-NaOH, soaked with 20 mM pNP-alpha-galactopyranoside
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.954 α = 90 b = 111.954 β = 90 c = 113.991 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 270 2014-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 2.1 50 99.3 0.091 24.1 9.7 42959
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 2.1 2.18 100 0.576 3.4 8.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XPO 2.1 50 39532 2066 97.05 0.19963 0.19707 0.2064 0.24906 0.2504 RANDOM 32.018
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_dihedral_angle_4_deg 16.607 r_dihedral_angle_3_deg 15.185 r_dihedral_angle_1_deg 6.622 r_long_range_B_refined 4.978 r_long_range_B_other 4.947 r_scangle_other 3.306 r_mcangle_it 2.558 r_mcangle_other 2.558 r_scbond_it 2.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.346 r_dihedral_angle_4_deg 16.607 r_dihedral_angle_3_deg 15.185 r_dihedral_angle_1_deg 6.622 r_long_range_B_refined 4.978 r_long_range_B_other 4.947 r_scangle_other 3.306 r_mcangle_it 2.558 r_mcangle_other 2.558 r_scbond_it 2.156 r_scbond_other 2.156 r_mcbond_it 1.745 r_mcbond_other 1.743 r_angle_refined_deg 1.438 r_angle_other_deg 0.781 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5332 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling MOLREP phasing