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Crystal Structure of NadC Deletion Mutant in C2221 Space Group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.4 293 20% PEG 6000, 0.1 M BIS-TRIS, 0.48 M Ammonium sulfate, 1.25 mM Sodium Bromide
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.203 α = 90 b = 186.261 β = 90 c = 221.906 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 MARMOSAIC 225 mm CCD 2014-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM
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 2.8 40 100 0.108 0.108 14.6 8.4 54566 -3
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 2.8 2.85 100 0.785 2.3 8.5
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 5HUL 2.8 40 51653 2766 99.92 0.21799 0.21599 0.2628 0.25539 0.3023 RANDOM 124.789
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] 3.92 -2.04 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.062 r_dihedral_angle_4_deg 22.212 r_dihedral_angle_3_deg 15.971 r_long_range_B_refined 8.026 r_long_range_B_other 8.017 r_dihedral_angle_1_deg 5.736 r_mcangle_it 4.396 r_mcangle_other 4.396 r_scangle_other 4.357 r_scbond_it 2.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.062 r_dihedral_angle_4_deg 22.212 r_dihedral_angle_3_deg 15.971 r_long_range_B_refined 8.026 r_long_range_B_other 8.017 r_dihedral_angle_1_deg 5.736 r_mcangle_it 4.396 r_mcangle_other 4.396 r_scangle_other 4.357 r_scbond_it 2.797 r_mcbond_it 2.635 r_mcbond_other 2.633 r_scbond_other 2.633 r_angle_other_deg 2.206 r_angle_refined_deg 1.543 r_chiral_restr 0.081 r_bond_refined_d 0.016 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12807 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing