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COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION with cellobio-derived isofagomine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A3H PDB ENTR 6A3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.2 PROTEIN WAS USED AT A CONCENTRATION OF 10MG/ML. IT WAS INCUBATED WITH 5MM CELLOBIO-DERIVED ISOFAGOMINE FOR AN HOUR PRIOR CRYSTALLISATION. THE VAPOR DIFFUSION METHOD WAS USED. 1.3 M AMMONIUM SULPHATE WERE USED AS PRECIPITANT. 20 % GLYCEROL WAS ADDED FOR CRYOPROTECTION, pH 5.20
Crystal Properties Matthews coefficient Solvent content 2.2 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.023 α = 90 b = 69.677 β = 90 c = 76.899 γ = 90
Symmetry Space Group P 21 21 21
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 2002-01-15 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 1.08 15 99.7 0.07 17.3 4.3 126591
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 1.08 1.1 99.9 0.377 3.8 4.1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTR 6A3H 1.08 14.96 119168 6322 99.1 0.115 0.115 0.1341 0.127 0.1472 RANDOM 9.47
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] 1.11 -0.53 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.433 r_scangle_it 3.876 r_scbond_it 2.69 r_angle_other_deg 2.13 r_mcangle_it 2.046 r_angle_refined_deg 1.766 r_mcbond_it 1.358 r_symmetry_vdw_other 0.274 r_nbd_other 0.273 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.433 r_scangle_it 3.876 r_scbond_it 2.69 r_angle_other_deg 2.13 r_mcangle_it 2.046 r_angle_refined_deg 1.766 r_mcbond_it 1.358 r_symmetry_vdw_other 0.274 r_nbd_other 0.273 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.123 r_nbtor_other 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.009 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2377 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing