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Structure of the R domain of carboxylic acid reductase (CAR) from Mycobacterium marinum in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Co-crystals of CARmm Red domain with NADP were obtained in 0.2 M sodium sulphate, 0.1 M Bis-Tris-propane pH 6.5, 20% PEG3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.242 α = 90 b = 136.156 β = 90 c = 115.488 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 PIXEL DECTRIS PILATUS 6M-F 2016-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.2 115.49 99 0.04 1 18 3.9 143907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 100 0.5
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 4DQV 1.2 115.49 136673 7234 94.28 0.13573 0.13486 0.141 0.15198 0.1579 RANDOM 21.396
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] -0.13 0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.021 r_sphericity_free 27.695 r_dihedral_angle_4_deg 18.604 r_sphericity_bonded 10.277 r_dihedral_angle_3_deg 10.147 r_dihedral_angle_1_deg 5.847 r_long_range_B_refined 3.156 r_long_range_B_other 3.156 r_scangle_other 2.345 r_rigid_bond_restr 2.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.021 r_sphericity_free 27.695 r_dihedral_angle_4_deg 18.604 r_sphericity_bonded 10.277 r_dihedral_angle_3_deg 10.147 r_dihedral_angle_1_deg 5.847 r_long_range_B_refined 3.156 r_long_range_B_other 3.156 r_scangle_other 2.345 r_rigid_bond_restr 2.061 r_scbond_it 1.842 r_scbond_other 1.842 r_mcangle_it 1.796 r_mcangle_other 1.796 r_angle_refined_deg 1.587 r_mcbond_it 1.407 r_mcbond_other 1.396 r_angle_other_deg 0.989 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3400 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing