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X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M9V PDB ENTRY 3M9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 25% pentaerythritol propoxylate 5/4
100 mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.828 α = 90 b = 81.297 β = 90 c = 152.628 γ = 90
Symmetry Space Group I 2 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 CCD ADSC QUANTUM 210r 2012-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.098 76.31 90.4 0.069 5.7 23596 23596
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.098 2.18 85.5 0.11 17.5 3.9 2209
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 3M9V 2.098 76.31 23596 1193 89.93 0.17742 0.17492 0.1769 0.22518 0.2287 RANDOM 33.777
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] 2.68 -0.93 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.001 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 15.195 r_dihedral_angle_1_deg 6.238 r_scangle_it 4.839 r_scbond_it 3.124 r_angle_refined_deg 2.269 r_mcangle_it 2.078 r_mcbond_it 1.218 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.001 r_dihedral_angle_4_deg 18.978 r_dihedral_angle_3_deg 15.195 r_dihedral_angle_1_deg 6.238 r_scangle_it 4.839 r_scbond_it 3.124 r_angle_refined_deg 2.269 r_mcangle_it 2.078 r_mcbond_it 1.218 r_chiral_restr 0.131 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3025 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 61
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling