☰ Navigation Tabs
Crystal structure of Apo acid-beta-glucosidase pH 4.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NT0 PDB entry 2NT0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 298 0.8 M Na H2PO4, 0.8 M K H2PO4, 0.1 M Citrate pH 5.5
soaked with acetate buffer pH 4.5 and 1.8 M Li2SO4 prior to freezing, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.442 α = 90 b = 91.703 β = 111.04 c = 152.491 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 2.5 142 81268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 2.1
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 THROUGHOUT PDB entry 2NT0 2.5 42.14 81268 4342 87.66 0.208 0.204 0.2046 0.275 0.2738 RANDOM 49.621
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] 0.08 0.06 -0.14 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.923 r_dihedral_angle_4_deg 23.621 r_dihedral_angle_3_deg 19.519 r_dihedral_angle_1_deg 7.851 r_scangle_it 3.501 r_scbond_it 2.223 r_angle_refined_deg 1.873 r_mcangle_it 1.668 r_mcbond_it 0.955 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.923 r_dihedral_angle_4_deg 23.621 r_dihedral_angle_3_deg 19.519 r_dihedral_angle_1_deg 7.851 r_scangle_it 3.501 r_scbond_it 2.223 r_angle_refined_deg 1.873 r_mcangle_it 1.668 r_mcbond_it 0.955 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15720 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 334
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection REFMAC phasing