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Crystal Structure of an Oxidoreductase from Agrobacterium radiobacter in Complex with NAD+ and Magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.5 M Sodium formate, 5 mM NAD+, 5 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.42 64.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.674 α = 90 b = 112.856 β = 95.02 c = 65.741 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 QUANTUM 315 Diamond 2016-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.24 19.98 99.1 0.095 0.131 0.09 0.989 6.5 3.7 48152
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.36 95.6 0.767 1.025 0.675 0.374 1.2 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3EZY 2.24 19.98 45754 2394 98.98 0.18942 0.18803 0.21601 0.2315 RANDOM 49.434
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] -1.03 -0.65 0.98 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.492 r_dihedral_angle_3_deg 14.821 r_dihedral_angle_4_deg 14.759 r_dihedral_angle_1_deg 6.189 r_long_range_B_refined 2.743 r_long_range_B_other 2.743 r_mcangle_it 1.535 r_mcangle_other 1.535 r_angle_refined_deg 1.491 r_scangle_other 1.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.492 r_dihedral_angle_3_deg 14.821 r_dihedral_angle_4_deg 14.759 r_dihedral_angle_1_deg 6.189 r_long_range_B_refined 2.743 r_long_range_B_other 2.743 r_mcangle_it 1.535 r_mcangle_other 1.535 r_angle_refined_deg 1.491 r_scangle_other 1.401 r_angle_other_deg 0.962 r_mcbond_other 0.864 r_mcbond_it 0.863 r_scbond_it 0.799 r_scbond_other 0.799 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5194 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 90
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement