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Structure of the unmodified PCP-R domain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADPH, P43 form
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 the condition 0.1 M sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.943 α = 90 b = 94.943 β = 90 c = 335.506 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 2016-07-16 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 2.37 200 99 0.13 1 6.4 5.6 112379
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 2.37 2.46 99.5 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 5MSO 2.37 200 112379 5667 98.65 0.2198 0.21869 0.2289 0.24127 0.2451 RANDOM 86.534
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 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.895 r_dihedral_angle_4_deg 15.368 r_dihedral_angle_3_deg 15.037 r_long_range_B_refined 10.575 r_long_range_B_other 10.575 r_scangle_other 7.86 r_mcangle_it 6.949 r_mcangle_other 6.948 r_dihedral_angle_1_deg 5.152 r_scbond_other 5.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.895 r_dihedral_angle_4_deg 15.368 r_dihedral_angle_3_deg 15.037 r_long_range_B_refined 10.575 r_long_range_B_other 10.575 r_scangle_other 7.86 r_mcangle_it 6.949 r_mcangle_other 6.948 r_dihedral_angle_1_deg 5.152 r_scbond_other 5.054 r_scbond_it 5.053 r_mcbond_it 4.662 r_mcbond_other 4.661 r_angle_refined_deg 1.337 r_angle_other_deg 1.258 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 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 15712 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing