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Apo Structure of Beta-1,3-1,4-glucanase from Paenibacillus sp.X4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 287 0.1M amino acids, 12.5%(v/v) MPD, 12.5%(w/v) PEG 1000, 12.5%(w/v) PEG 3350, 0.1 M Tris(base)/Bicine
Crystal Properties Matthews coefficient Solvent content 2.3 42.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.721 α = 71.04 b = 64.161 β = 77.07 c = 70.502 γ = 75.6
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 QUANTUM 315r 2015-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 65.86 97.5 25 3.6 66856
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 1.8 1.83 96.3 0.379 4.8 3.6
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 1V5C 1.79 65.86 63477 3379 96.4 0.15283 0.15098 0.1633 0.18761 0.1953 RANDOM 14.798
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.254 r_dihedral_angle_4_deg 17.23 r_dihedral_angle_3_deg 13.73 r_dihedral_angle_1_deg 6.187 r_long_range_B_refined 3.899 r_long_range_B_other 3.866 r_scangle_other 3.159 r_scbond_it 2.102 r_scbond_other 2.098 r_mcangle_it 1.917
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.254 r_dihedral_angle_4_deg 17.23 r_dihedral_angle_3_deg 13.73 r_dihedral_angle_1_deg 6.187 r_long_range_B_refined 3.899 r_long_range_B_other 3.866 r_scangle_other 3.159 r_scbond_it 2.102 r_scbond_other 2.098 r_mcangle_it 1.917 r_mcangle_other 1.917 r_angle_refined_deg 1.859 r_mcbond_it 1.32 r_mcbond_other 1.318 r_angle_other_deg 1.156 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5860 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing