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Crystal structure of Arthrobacter globiformis M30 sugar epimerase which can produce D-allulose from D-fructose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 AMMONIUM ACETATE, SODIUM ACETATE TRIHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 3.08 60.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.98 α = 90 b = 103.98 β = 90 c = 256.53 γ = 120
Symmetry Space Group P 65 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 PILATUS 2M-F 2016-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.96 45.02 99 0.078 0.08 0.999 31.46 22.556 59179 28.637
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 91.5 0.33 0.369 0.908 4.59 4.652
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 3VYL 1.96 45.02 56104 2980 99.01 0.1869 0.1856 0.193 0.2111 0.2204 RANDOM 23.161
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_4_deg 21.973 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 6.743 r_angle_refined_deg 0.718 r_angle_other_deg 0.525 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_4_deg 21.973 r_dihedral_angle_3_deg 14.661 r_dihedral_angle_1_deg 6.743 r_angle_refined_deg 0.718 r_angle_other_deg 0.525 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4486 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing