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Active-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UR7 PDB ENTRY 3UR7
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, 0.2 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.09 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.895 α = 90 b = 49.273 β = 98.38 c = 57.075 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 2006-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.81620 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 1.68 30 99 0.069 23.2 6.2 34231 34231 -3 24.6
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 1.68 1.74 92.7 0.264 5.1 4.8 3131
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R-FREE PDB ENTRY 3UR7 1.68 20 -3 33126 33126 1076 99.04 0.1375 0.1375 0.1364 0.1713 0.1974 RANDOM 17.54
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] -0.06 -1.05 -0.82 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.25 r_dihedral_angle_4_deg 15.453 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.885 r_scbond_it 2.769 r_angle_refined_deg 1.567 r_mcangle_it 1.55 r_mcbond_it 1.363 r_angle_other_deg 0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.25 r_dihedral_angle_4_deg 15.453 r_dihedral_angle_3_deg 11.751 r_dihedral_angle_1_deg 6.233 r_scangle_it 3.885 r_scbond_it 2.769 r_angle_refined_deg 1.567 r_mcangle_it 1.55 r_mcbond_it 1.363 r_angle_other_deg 0.884 r_mcbond_other 0.303 r_symmetry_vdw_other 0.225 r_nbd_refined 0.215 r_nbtor_refined 0.184 r_nbd_other 0.177 r_symmetry_vdw_refined 0.135 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.11 r_nbtor_other 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 338 Heterogen Atoms 34
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling