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Crystallization of B. licheniformis levanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 10% w/v PEG 8000, 20% v/v ethylene glycol and 0.03 M Magnesium chloride, calcium chloride and 0.1 M bicine/Trizma base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.87 57.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.586 α = 90 b = 82.586 β = 90 c = 171.088 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.5 74.375 97.1 0.999 15.9 26.1 85690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 0.698 0.639
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4fff 1.54 74.375 85314 4272 96.772 0.194 0.1928 0.204 0.2169 0.2288 23.445
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] -0.132 -0.132 0.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.398 r_dihedral_angle_3_deg 12.529 r_lrange_it 8.627 r_lrange_other 8.626 r_dihedral_angle_1_deg 7.197 r_dihedral_angle_2_deg 6.503 r_scangle_it 6.481 r_scangle_other 6.48 r_scbond_it 4.193 r_scbond_other 4.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.398 r_dihedral_angle_3_deg 12.529 r_lrange_it 8.627 r_lrange_other 8.626 r_dihedral_angle_1_deg 7.197 r_dihedral_angle_2_deg 6.503 r_scangle_it 6.481 r_scangle_other 6.48 r_scbond_it 4.193 r_scbond_other 4.192 r_mcangle_other 3.709 r_mcangle_it 3.705 r_mcbond_it 2.533 r_mcbond_other 2.509 r_angle_refined_deg 1.815 r_angle_other_deg 0.63 r_symmetry_nbd_refined 0.38 r_nbd_other 0.268 r_symmetry_nbd_other 0.199 r_nbd_refined 0.198 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.099 r_chiral_restr 0.094 r_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_symmetry_metal_ion_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_chiral_restr_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3583 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction MrBUMP phasing SCALA data scaling