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Crystal structure of human beta-galactosidase in complex with galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 20% (w/v) PEG3350
0.2M ammonium sulfate, 100mM Tris HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.799 α = 90 b = 116.104 β = 92.21 c = 140.326 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 95 CCD ADSC QUANTUM 270 2009-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 28.88 78 3.3 250825
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 3D3A 1.8 28.88 250825 13359 94.14 0.19217 0.19027 0.1922 0.22833 0.2292 RANDOM 19.407
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] 0.02 -0.01 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.722 r_dihedral_angle_4_deg 18.863 r_dihedral_angle_3_deg 14.469 r_dihedral_angle_1_deg 6.389 r_angle_refined_deg 1.43 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.722 r_dihedral_angle_4_deg 18.863 r_dihedral_angle_3_deg 14.469 r_dihedral_angle_1_deg 6.389 r_angle_refined_deg 1.43 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 19198 Nucleic Acid Atoms Solvent Atoms 2242 Heterogen Atoms 348
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling