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Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 16-18% PEG 8K, 3% MPD, 0.1M imidazole buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.158 α = 90 b = 68.944 β = 100.39 c = 152.896 γ = 90
Symmetry Space Group C 1 2 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 2014-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.21 50 99.5 0.085 11.4 3.9 55496
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 2.21 2.25 94.7 0.301 3.3 3.2
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 4ZE4 2.21 28.31 52090 2788 98.89 0.15354 0.15068 0.1592 0.20703 0.2092 RANDOM 34.236
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] 3.44 0.85 -1.68 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.423 r_dihedral_angle_4_deg 17.604 r_dihedral_angle_3_deg 14.422 r_long_range_B_refined 7.009 r_long_range_B_other 7.008 r_dihedral_angle_1_deg 6.698 r_scangle_other 5.54 r_mcangle_it 3.874 r_mcangle_other 3.873 r_scbond_it 3.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.423 r_dihedral_angle_4_deg 17.604 r_dihedral_angle_3_deg 14.422 r_long_range_B_refined 7.009 r_long_range_B_other 7.008 r_dihedral_angle_1_deg 6.698 r_scangle_other 5.54 r_mcangle_it 3.874 r_mcangle_other 3.873 r_scbond_it 3.652 r_scbond_other 3.652 r_mcbond_it 2.775 r_mcbond_other 2.775 r_angle_refined_deg 1.799 r_angle_other_deg 0.914 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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 7748 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing