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Structure of Gan1D-E170Q, a catalytic mutant of a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 16-18% PEG 8K, 3% MPD, 0.1 M imidazole buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.55 α = 90 b = 97.44 β = 97.82 c = 105.24 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.98 ESRF BM14
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 1.48 35 99.7 0.067 12.6 5.7 337040
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 1.48 1.51 94.9 0.375 3.9 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZEH 1.48 27.64 319084 16966 99.71 0.13346 0.1321 0.1317 0.15929 0.1587 RANDOM 14.232
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] -0.6 0.17 0.63 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.197 r_dihedral_angle_4_deg 17.05 r_dihedral_angle_3_deg 11.911 r_long_range_B_refined 7.126 r_long_range_B_other 7.126 r_dihedral_angle_1_deg 6.972 r_scangle_other 4.323 r_scbond_it 2.894 r_scbond_other 2.894 r_mcangle_it 2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.197 r_dihedral_angle_4_deg 17.05 r_dihedral_angle_3_deg 11.911 r_long_range_B_refined 7.126 r_long_range_B_other 7.126 r_dihedral_angle_1_deg 6.972 r_scangle_other 4.323 r_scbond_it 2.894 r_scbond_other 2.894 r_mcangle_it 2.73 r_mcangle_other 2.73 r_angle_refined_deg 2.504 r_mcbond_it 1.794 r_mcbond_other 1.794 r_angle_other_deg 1.055 r_chiral_restr 0.156 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 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 15110 Nucleic Acid Atoms Solvent Atoms 2556 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing