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Protein crystallization by ionic liquid hydrogel support: reference crystal of glucose isomerase grown on standard silanized glass
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 Protein concentration 26mg/ml in HEPES 10mM pH 7 and MgCl2 1mM.
reservoir: (NH4)2SO4 1.5M
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.522 α = 90 b = 98.167 β = 90 c = 101.851 γ = 90
Symmetry Space Group I 2 2 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 EIGER X 16M 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97779 Diamond I04
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 1.19 39.93 76.7 0.042 0.049 0.03 0.999 14.7 3.4 112879 8.59
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 1.19 1.22 4.9 0.166 0.234 0.166 0.966 2.6 1
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 1OAD 1.19 39.93 107045 5749 76.54 0.10775 0.10659 0.1066 0.12943 0.1295 RANDOM 13.397
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 -0.07 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.146 r_rigid_bond_restr 26.141 r_dihedral_angle_4_deg 17.604 r_long_range_B_other 15.341 r_long_range_B_refined 15.26 r_dihedral_angle_3_deg 11.642 r_scangle_other 10.845 r_scbond_other 10.189 r_scbond_it 10.186 r_mcangle_other 8.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.146 r_rigid_bond_restr 26.141 r_dihedral_angle_4_deg 17.604 r_long_range_B_other 15.341 r_long_range_B_refined 15.26 r_dihedral_angle_3_deg 11.642 r_scangle_other 10.845 r_scbond_other 10.189 r_scbond_it 10.186 r_mcangle_other 8.573 r_mcangle_it 8.571 r_mcbond_it 6.968 r_mcbond_other 6.966 r_dihedral_angle_1_deg 6.665 r_angle_other_deg 1.517 r_angle_refined_deg 1.347 r_chiral_restr 0.063 r_gen_planes_refined 0.018 r_gen_planes_other 0.008 r_bond_refined_d 0.004 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3033 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 25
Software Software Software Name Purpose xia2 data reduction Aimless data scaling Sir2014 phasing REFMAC refinement BUSTER-TNT refinement