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acid-beta-glucosidase produced in carrot
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGS PDB ENTRY 1OGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 AMSO4 0.2M, BIS-TRIS PH6.5, PEG 3350 25%, HEXAMINECOCL
Crystal Properties Matthews coefficient Solvent content 2.3 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.088 α = 90 b = 97.104 β = 104.43 c = 82.932 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 ADSC CCD MIRRORD 2005-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.95 50 97 0.1 13.6 4 74750
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 1.95 1.98 98.9 0.25 6.3 3.9
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 PDB ENTRY 1OGS 1.95 41.56 66326 7449 96.9 0.154 0.149 0.1513 0.196 0.1976 RANDOM 13.6
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.897 r_dihedral_angle_4_deg 21.089 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 7.556 r_scangle_it 3.057 r_scbond_it 2.027 r_angle_refined_deg 1.371 r_mcangle_it 1.313 r_mcbond_it 0.85 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.897 r_dihedral_angle_4_deg 21.089 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 7.556 r_scangle_it 3.057 r_scbond_it 2.027 r_angle_refined_deg 1.371 r_mcangle_it 1.313 r_mcbond_it 0.85 r_nbtor_refined 0.308 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.16 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.096 r_bond_refined_d 0.014 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 7759 Nucleic Acid Atoms Solvent Atoms 805 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing