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Lower-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 3UR7 PDB ENTRY 3UR7
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 2.03 39.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.361 α = 90 b = 49.056 β = 103.56 c = 82.618 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 0.8148 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 1.26 40 95.4 0.059 19.2 4.6 151662 151662 -3 12.9
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 1.26 1.31 93.8 0.467 2 3.3 14787
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 3UR7 1.26 19.54 149903 149903 1654 95.04 0.14277 0.14277 0.14235 0.143 0.18244 0.181 RANDOM 9.348
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 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_4_deg 15.339 r_dihedral_angle_3_deg 11.999 r_sphericity_free 10.821 r_dihedral_angle_1_deg 6.297 r_sphericity_bonded 5.096 r_scangle_it 4.627 r_scbond_it 3.554 r_mcangle_it 2.493 r_mcbond_it 2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_4_deg 15.339 r_dihedral_angle_3_deg 11.999 r_sphericity_free 10.821 r_dihedral_angle_1_deg 6.297 r_sphericity_bonded 5.096 r_scangle_it 4.627 r_scbond_it 3.554 r_mcangle_it 2.493 r_mcbond_it 2.097 r_rigid_bond_restr 1.807 r_angle_refined_deg 1.744 r_angle_other_deg 1.044 r_mcbond_other 0.933 r_symmetry_vdw_other 0.264 r_nbd_refined 0.22 r_nbtor_refined 0.191 r_nbd_other 0.173 r_symmetry_vdw_refined 0.156 r_chiral_restr 0.119 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.111 r_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5091 Nucleic Acid Atoms Solvent Atoms 763 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling