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Structure of Caenorhabditis Elegans UDP-Glucose Dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DLI pdb entry 1DLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 200 MM MgCl2, 100 MM BIS-TRIS, PH 5.50, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.8 56.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.716 α = 90 b = 144.092 β = 123.24 c = 92.072 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 MIRRORS 2006-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.88 50 98.7 0.064 0.057 2.7 2.7 133254 34.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.95 90.4 0.73 0.71 0.8 2.1 25057
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 1DLI 1.88 20 133254 133254 4145 98.17 0.2102 0.20858 0.2075 0.26315 0.2591 RANDOM 45.475
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] -2.26 -1.11 1.47 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.866 r_dihedral_angle_3_deg 17.826 r_dihedral_angle_4_deg 14.668 r_scangle_it 9.903 r_dihedral_angle_1_deg 7.534 r_scbond_it 7.42 r_mcangle_it 6.026 r_mcbond_it 4.874 r_angle_refined_deg 1.114 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.866 r_dihedral_angle_3_deg 17.826 r_dihedral_angle_4_deg 14.668 r_scangle_it 9.903 r_dihedral_angle_1_deg 7.534 r_scbond_it 7.42 r_mcangle_it 6.026 r_mcbond_it 4.874 r_angle_refined_deg 1.114 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.175 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.156 r_chiral_restr 0.104 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10719 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 54
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling