☰ Navigation Tabs
Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5U4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 200 mM potassium acetate and 14-24% PEG 3350, 2 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.482 α = 96.77 b = 58.56 β = 98.41 c = 64.904 γ = 110.3
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 2019-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.98 SLS X06SA
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 1.7 45.35 93 0.99 10.2 1.7 55496
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 1.7 1.74 0.88
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 5U4Q 1.7 45.35 55496 2872 92.96 0.1722 0.1707 0.1804 0.2025 0.2107 RANDOM 25.573
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] -0.27 0.42 -0.34 0.2 0.82 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.125 r_dihedral_angle_3_deg 13.828 r_dihedral_angle_4_deg 12.585 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.675 r_angle_other_deg 1.415 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.125 r_dihedral_angle_3_deg 13.828 r_dihedral_angle_4_deg 12.585 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.675 r_angle_other_deg 1.415 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4932 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing