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Higher-density crystal structure of potato endo-1,3-beta-glucanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GHS PDB ENTRY 1GHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 292 0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.96 37.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.128 α = 90 b = 49.133 β = 102.4 c = 80.504 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 MAR CCD 165 mm mirrors 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04300 MAX II I911-2
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 1.4 30 100 0.071 20.1 4.5 110982 110982 -3 27.1
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 1.4 1.45 100 0.49 2.7 3.1 11024
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1GHS 1.4 20 109834 109834 1117 99.66 0.16153 0.16153 0.16128 0.1738 0.1859 0.2016 RANDOM 16.815
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] -1.45 0.24 -1.38 2.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.631 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 12.074 r_sphericity_free 10.357 r_sphericity_bonded 6.286 r_dihedral_angle_1_deg 6.271 r_scangle_it 5.136 r_scbond_it 3.625 r_mcangle_it 2.691 r_mcbond_it 1.897
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.631 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 12.074 r_sphericity_free 10.357 r_sphericity_bonded 6.286 r_dihedral_angle_1_deg 6.271 r_scangle_it 5.136 r_scbond_it 3.625 r_mcangle_it 2.691 r_mcbond_it 1.897 r_angle_refined_deg 1.731 r_rigid_bond_restr 1.706 r_mcbond_other 1.104 r_angle_other_deg 0.935 r_symmetry_vdw_other 0.223 r_nbd_refined 0.219 r_nbtor_refined 0.182 r_nbd_other 0.171 r_symmetry_hbond_refined 0.161 r_symmetry_vdw_refined 0.151 r_chiral_restr 0.123 r_xyhbond_nbd_refined 0.113 r_metal_ion_refined 0.096 r_nbtor_other 0.085 r_symmetry_metal_ion_refined 0.048 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5046 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 1
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling