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Structure of the A-PCP didomain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 A-PCP crystals were obtained in 0.2 M sodium fluoride, 0.1 M Bis-Tris Propane pH 6.5 and 20% PEG3350.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.42 α = 90 b = 65.33 β = 110.8 c = 101.71 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 PIXEL DECTRIS PILATUS 6M-F 2016-07-20 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 2.33 95.08 99 0.09 1 10.9 2.8 34371
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 2.33 2.41 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 5MSQ 2.33 95.08 32634 1738 99.05 0.19602 0.19352 0.2019 0.24337 0.2472 RANDOM 47.076
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] 1.06 0.33 -2.43 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_dihedral_angle_4_deg 20.382 r_dihedral_angle_3_deg 17.473 r_long_range_B_other 8.494 r_long_range_B_refined 8.489 r_dihedral_angle_1_deg 6.754 r_scangle_other 6.506 r_mcangle_it 5.198 r_mcangle_other 5.198 r_scbond_it 4.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_dihedral_angle_4_deg 20.382 r_dihedral_angle_3_deg 17.473 r_long_range_B_other 8.494 r_long_range_B_refined 8.489 r_dihedral_angle_1_deg 6.754 r_scangle_other 6.506 r_mcangle_it 5.198 r_mcangle_other 5.198 r_scbond_it 4.123 r_scbond_other 4.122 r_mcbond_it 3.501 r_mcbond_other 3.498 r_angle_refined_deg 1.717 r_angle_other_deg 1.035 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5431 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing