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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 CARsr Ade-PCP (thiolation state) crystals were grown in 1.5 M Lithium Sulphate and 0.1 M HePES pH 7.5.
Crystal Properties Matthews coefficient Solvent content 1.58 21.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.719 α = 90 b = 127.693 β = 90 c = 212.244 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 2016-07-15 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 1.96 106.12 99 0.08 1 10.2 4.86 58078
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 1.96 2.03 99.5 0.6
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 5MSQ 1.96 106.12 55167 2911 98.98 0.20657 0.20407 0.2126 0.25421 0.2604 RANDOM 30.685
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] -0.02 0.06 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_4_deg 16.683 r_dihedral_angle_3_deg 15.065 r_dihedral_angle_1_deg 6.56 r_angle_refined_deg 1.9 r_angle_other_deg 0.914 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.335 r_dihedral_angle_4_deg 16.683 r_dihedral_angle_3_deg 15.065 r_dihedral_angle_1_deg 6.56 r_angle_refined_deg 1.9 r_angle_other_deg 0.914 r_chiral_restr 0.107 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 5450 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing