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Structure of the phosphopantetheine modified PCP-R didomain of carboxylic acid reductase (CAR) in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MSO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 CARsr PCP-Red crystals were obtained in 0.1 M carboxylic acids 0.1M, Buffer system 1 pH 6.5, 50% Precipitant Mix 2 of Morpheus screen.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.11 α = 90 b = 92.11 β = 90 c = 363.5 γ = 90
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 2016-10-04 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 2.34 200 95 0.12 1 11.3 6.8 120649
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 2.34 2.42 92.3 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MSO 2.34 200 114730 5923 95.24 0.19223 0.19143 0.2075 0.1901 RANDOM 44.473
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] -0.53 -0.53 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 14.759 r_long_range_B_refined 6.481 r_long_range_B_other 6.48 r_dihedral_angle_1_deg 5.282 r_scangle_other 5.148 r_mcangle_it 3.529 r_mcangle_other 3.529 r_scbond_it 3.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.422 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 14.759 r_long_range_B_refined 6.481 r_long_range_B_other 6.48 r_dihedral_angle_1_deg 5.282 r_scangle_other 5.148 r_mcangle_it 3.529 r_mcangle_other 3.529 r_scbond_it 3.283 r_scbond_other 3.283 r_mcbond_it 2.349 r_mcbond_other 2.348 r_angle_refined_deg 1.367 r_angle_other_deg 1.269 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 15747 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing