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Crystal structure of RasADH F12 from Ralstonia.sp in complex with NADPH and A6O
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 Ammonium Sulfate, Bis-Tris, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.79 61.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.687 α = 90 b = 118.687 β = 90 c = 73.009 γ = 120
Symmetry Space Group P 32 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 315r 2018-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 25 99.4 0.099 0.105 0.033 7 10.2 55225
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 1.8 1.86 93.6 0.613 0.65 0.214 0.947 8.6
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 4bms 1.8 24.35 52388 2695 99.87 0.16828 0.16642 0.1678 0.20393 0.2049 RANDOM 34.053
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] 1.2 0.6 1.2 -3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.602 r_dihedral_angle_3_deg 13.971 r_dihedral_angle_4_deg 13.949 r_long_range_B_refined 10.542 r_dihedral_angle_1_deg 7.441 r_scbond_it 6.866 r_mcangle_it 5.783 r_mcbond_it 4.5 r_angle_refined_deg 1.576 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.602 r_dihedral_angle_3_deg 13.971 r_dihedral_angle_4_deg 13.949 r_long_range_B_refined 10.542 r_dihedral_angle_1_deg 7.441 r_scbond_it 6.866 r_mcangle_it 5.783 r_mcbond_it 4.5 r_angle_refined_deg 1.576 r_chiral_restr 0.111 r_gen_planes_refined 0.018 r_bond_refined_d 0.009 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 3750 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing