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Structure of the PN loop Q182A mutant C3bot1 Exoenzyme (NAD-bound state, crystal form I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZF PDB ENTRY 1GZF
Crystallization Crystal Properties Matthews coefficient Solvent content 2.31 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.388 α = 90 b = 75.611 β = 102.75 c = 120.783 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.65 31.78 96.7 0.06 18.6 4 107532 2
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 1GZF 1.65 31.78 102165 5365 100 0.218 0.216 0.2228 0.259 0.2661 RANDOM 26.03
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] 0.56 -0.22 0.62 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.282 r_scangle_it 2.285 r_scbond_it 1.356 r_angle_refined_deg 1.027 r_mcangle_it 0.946 r_angle_other_deg 0.721 r_mcbond_it 0.491 r_nbd_other 0.224 r_symmetry_vdw_other 0.188 r_nbd_refined 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.282 r_scangle_it 2.285 r_scbond_it 1.356 r_angle_refined_deg 1.027 r_mcangle_it 0.946 r_angle_other_deg 0.721 r_mcbond_it 0.491 r_nbd_other 0.224 r_symmetry_vdw_other 0.188 r_nbd_refined 0.185 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.111 r_nbtor_other 0.08 r_symmetry_vdw_refined 0.076 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 6425 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing