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Structure of a glucose isomerase crystal grown in an aqueous glycerol solution without any precipitants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 precipitant-free in 30(v/v)% aqueous glycerol solution
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.61 α = 90 b = 98.46 β = 90 c = 102.3 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 90 PIXEL DECTRIS EIGER X 16M 2019-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 0.99 70.94 99.8 0.046 0.998 16.9 6.4 256074
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.01 0.308 0.94
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 1XIB 0.99 51.16 242981 13077 99.73 0.15736 0.15693 0.1669 0.16564 0.174 RANDOM 9.953
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] -0.19 0.36 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.056 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 10.761 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 3.626 r_long_range_B_other 3.532 r_scangle_other 3.193 r_scbond_it 2.307 r_scbond_other 2.303 r_angle_refined_deg 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.056 r_dihedral_angle_4_deg 16.98 r_dihedral_angle_3_deg 10.761 r_dihedral_angle_1_deg 5.69 r_long_range_B_refined 3.626 r_long_range_B_other 3.532 r_scangle_other 3.193 r_scbond_it 2.307 r_scbond_other 2.303 r_angle_refined_deg 2.29 r_mcangle_other 1.292 r_mcangle_it 1.284 r_angle_other_deg 1.124 r_mcbond_it 0.953 r_mcbond_other 0.921 r_chiral_restr 0.13 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 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 3039 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling MOLREP phasing