☰ Navigation Tabs
Crystal structure of Codakine in complex with biantennary nonasaccharide at 1.7A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VUV PDB ENTRY 2VUV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M LITHIUM SULFATE IN 100 MM SODIUM ACETATE PH 7.5 WITH 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.163 α = 90 b = 100.197 β = 90 c = 95.738 γ = 90
Symmetry Space Group C 2 2 21
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 CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 34.6 98.6 0.08 5.3 5.6 17204 2 19.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 99.3 0.38 2 5.7
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 PDB ENTRY 2VUV 1.7 50.13 16302 874 98.2 0.204 0.202 0.2043 0.258 0.2564 RANDOM 18.48
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] 1.28 0.52 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.288 r_dihedral_angle_3_deg 14.863 r_dihedral_angle_4_deg 10.068 r_dihedral_angle_1_deg 6.997 r_scangle_it 3.25 r_scbond_it 2.306 r_mcangle_it 1.792 r_angle_refined_deg 1.763 r_mcbond_it 1.141 r_angle_other_deg 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.288 r_dihedral_angle_3_deg 14.863 r_dihedral_angle_4_deg 10.068 r_dihedral_angle_1_deg 6.997 r_scangle_it 3.25 r_scbond_it 2.306 r_mcangle_it 1.792 r_angle_refined_deg 1.763 r_mcbond_it 1.141 r_angle_other_deg 0.98 r_symmetry_vdw_refined 0.388 r_symmetry_vdw_other 0.254 r_nbd_refined 0.211 r_nbd_other 0.2 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.103 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 997 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing