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Trametes ljubarskyi GH12 endoglucanase - native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 50% MPD, 20% tBuOH
Crystal Properties Matthews coefficient Solvent content 3.18 61.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.824 α = 90 b = 50.104 β = 90 c = 140.25 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2020-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.1 42.7 96 0.05 0.054 0.021 1 15.1 12.2 123586
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.1 1.12 70 3.085 3.553 1.717 0.297 0.4 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.1 42.696 123331 6187 95.637 0.148 0.1476 0.1476 0.1646 0.1646 RANDOM 21.662
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] 0.3 0.24 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.718 r_lrange_it 11.896 r_dihedral_angle_3_deg 11.046 r_scangle_it 9.465 r_dihedral_angle_2_deg 7.736 r_dihedral_angle_1_deg 7.545 r_scbond_it 7.269 r_mcangle_it 7.068 r_rigid_bond_restr 5.684 r_mcbond_it 5.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.718 r_lrange_it 11.896 r_dihedral_angle_3_deg 11.046 r_scangle_it 9.465 r_dihedral_angle_2_deg 7.736 r_dihedral_angle_1_deg 7.545 r_scbond_it 7.269 r_mcangle_it 7.068 r_rigid_bond_restr 5.684 r_mcbond_it 5.198 r_angle_refined_deg 1.962 r_nbtor_refined 0.308 r_nbd_refined 0.255 r_symmetry_nbd_refined 0.197 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.137 r_symmetry_xyhbond_nbd_refined 0.07 r_bond_refined_d 0.013 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1745 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction MOLREP phasing