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The crystal structure of human cytosolic beta-glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V02 PDB ENTRY 1V02
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 CRYSTALS GREW WITHIN SEVERAL DAYS IN THE CRYSTALLIZATION TRIAL CONTAINING 0.2 M AMMONIUM SULPHATE, MES BUFFER AT PH 6.5 AND 30 % (W/V) POLYETHYLENEGLYCOL-MONOMETHYLETHER (PEG-MME) 5500
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.479 α = 90 b = 90.479 β = 90 c = 127.925 γ = 120
Symmetry Space Group P 31 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 ADSC CCD 2005-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.7 45 99.9 0.18 10.6 5.6 17144 1
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 2.7 2.79 100 0.67 3.1 5.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1V02 2.7 42.64 16273 865 100 0.201 0.197 0.2031 0.28 RANDOM 38.04
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] 1.42 0.71 1.42 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.192 r_dihedral_angle_3_deg 19.646 r_dihedral_angle_4_deg 19.547 r_dihedral_angle_1_deg 8.956 r_scangle_it 2.336 r_angle_refined_deg 1.632 r_scbond_it 1.522 r_mcangle_it 1.097 r_mcbond_it 0.618 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.192 r_dihedral_angle_3_deg 19.646 r_dihedral_angle_4_deg 19.547 r_dihedral_angle_1_deg 8.956 r_scangle_it 2.336 r_angle_refined_deg 1.632 r_scbond_it 1.522 r_mcangle_it 1.097 r_mcbond_it 0.618 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.261 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.21 r_chiral_restr 0.12 r_bond_refined_d 0.013 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3725 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing