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Active-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose and laminaratetrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GZI PDB ENTRY 4GZI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 0.1 M sodium citrate, 0.2 M ammonium acetate, 24% PEG 8000, 0.4 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.307 α = 90 b = 49.202 β = 98.84 c = 57.431 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 IMAGE PLATE MAR555 FLAT PANEL mirrors 2007-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81480 EMBL/DESY, HAMBURG X11
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 1.55 40 100 0.091 15.3 3.8 44391 44391 -3 21.2
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 1.55 1.61 100 0.68 2.1 3.8 4390
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 R-FREE PDB ENTRY 4GZI 1.55 20 -3 43213 43213 1139 99.91 0.1515 0.1515 0.1507 0.1642 0.1806 0.1839 RANDOM 15.27
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] -0.01 -0.47 -0.49 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_4_deg 15.502 r_dihedral_angle_3_deg 11.925 r_dihedral_angle_1_deg 6.2 r_scangle_it 3.674 r_scbond_it 2.47 r_angle_refined_deg 1.644 r_mcangle_it 1.592 r_mcbond_it 1.051 r_angle_other_deg 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_4_deg 15.502 r_dihedral_angle_3_deg 11.925 r_dihedral_angle_1_deg 6.2 r_scangle_it 3.674 r_scbond_it 2.47 r_angle_refined_deg 1.644 r_mcangle_it 1.592 r_mcbond_it 1.051 r_angle_other_deg 0.887 r_mcbond_other 0.32 r_nbd_refined 0.218 r_symmetry_vdw_other 0.195 r_nbtor_refined 0.19 r_nbd_other 0.173 r_symmetry_vdw_refined 0.134 r_symmetry_hbond_refined 0.125 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.11 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2509 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 57
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling