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6-phospho-beta-glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B3K PDB ENTRY 4B3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.33 MM SPY1599 WAS REACTED WITH 4.2 MM 6-PHOSPHO-CYCLOPHELLITOL EPOXIDE IN THE BUFFER OF 50 MM HEPES AND 150 MM NACL, PH 7.0, BEFORE BEING MIXED WITH THE SAME VOLUME OF BUFFER OF 0.1 M BIS TRIS PROPANE PH7.5, 20% PEG 3350 AND 0.15 M NABR
Crystal Properties Matthews coefficient Solvent content 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.017 α = 90 b = 109.899 β = 92.02 c = 158.5 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 293 PIXEL DECTRIS PILATUS 6M 2014-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.1 49.47 99.9 0.07 12.6 4.2 205534 1.9
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 2.1 2.14 99.9 0.62 1.9 4.2
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 PDB ENTRY 4B3K 2.1 158.4 195049 10459 99.91 0.17625 0.17385 0.1831 0.21989 0.2252 RANDOM 36.306
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] 0.99 -0.15 0.43 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.726 r_dihedral_angle_4_deg 17.969 r_dihedral_angle_3_deg 14.118 r_dihedral_angle_1_deg 10.899 r_mcangle_it 3.755 r_scbond_it 3.628 r_mcbond_it 2.891 r_mcbond_other 2.889 r_angle_refined_deg 1.843 r_angle_other_deg 1.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.726 r_dihedral_angle_4_deg 17.969 r_dihedral_angle_3_deg 14.118 r_dihedral_angle_1_deg 10.899 r_mcangle_it 3.755 r_scbond_it 3.628 r_mcbond_it 2.891 r_mcbond_other 2.889 r_angle_refined_deg 1.843 r_angle_other_deg 1.116 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it 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 22644 Nucleic Acid Atoms Solvent Atoms 981 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing