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The Crystal Structure of D-psicose-3-epimerase from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VNI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.02M MgCl2, 0.1M HEPES pH7.5, 22% Polyacrylic acid sodium salt 5,100
Crystal Properties Matthews coefficient Solvent content 3.11 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.134 α = 90 b = 116.083 β = 105.083 c = 91.817 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.5215 CLSI 08ID-1
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 2.1 48.607 98 0.998 10.2 3.4 91449
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.829
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 3vni 2.1 48.607 91439 4559 97.957 0.175 0.1737 0.1812 0.2058 0.2111 34.161
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] 0.358 1.476 -0.369 -0.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.172 r_dihedral_angle_4_deg 15.004 r_dihedral_angle_3_deg 13.96 r_dihedral_angle_1_deg 6.544 r_lrange_it 4.53 r_lrange_other 4.434 r_scangle_it 2.912 r_scangle_other 2.912 r_mcangle_it 2.327 r_mcangle_other 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.172 r_dihedral_angle_4_deg 15.004 r_dihedral_angle_3_deg 13.96 r_dihedral_angle_1_deg 6.544 r_lrange_it 4.53 r_lrange_other 4.434 r_scangle_it 2.912 r_scangle_other 2.912 r_mcangle_it 2.327 r_mcangle_other 2.326 r_scbond_it 1.873 r_scbond_other 1.872 r_mcbond_it 1.441 r_mcbond_other 1.44 r_angle_refined_deg 1.22 r_angle_other_deg 1.193 r_nbd_refined 0.187 r_nbd_other 0.176 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.118 r_symmetry_xyhbond_nbd_refined 0.084 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9212 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing