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X-ray Structure of a KijD3 in Complex with dTDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house MIR model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 1.3-1.6 M Ammonium Sulfate
10 mM dTDP-phenol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.948 α = 90 b = 82.487 β = 90 c = 153.22 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 277 AREA DETECTOR SIEMENS HI-STAR Supper Mirrors 2010-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 2.05 50 94.2 0.081 0.081 10.73 3.49 29420 27721
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) 2.05 2.15 80.7 0.196 0.196 3.5 1.5
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 In-house MIR model 2.05 50 27721 26300 1420 94.22 0.17108 0.1684 0.164 0.22107 0.2143 RANDOM 27.914
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] 1.08 -0.12 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.216 r_dihedral_angle_4_deg 18.061 r_dihedral_angle_3_deg 15.898 r_scangle_it 6.828 r_dihedral_angle_1_deg 6.338 r_scbond_it 4.327 r_mcangle_it 2.601 r_angle_refined_deg 1.995 r_mcbond_it 1.697 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.216 r_dihedral_angle_4_deg 18.061 r_dihedral_angle_3_deg 15.898 r_scangle_it 6.828 r_dihedral_angle_1_deg 6.338 r_scbond_it 4.327 r_mcangle_it 2.601 r_angle_refined_deg 1.995 r_mcbond_it 1.697 r_chiral_restr 0.137 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 2886 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 25
Software Software Software Name Purpose FRAMBO data collection PHASER phasing REFMAC refinement SAINT data reduction SADABS data scaling