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Structure of the R domain of carboxylic acid reductase (CAR) from Mycobacterium marinum in complex with NADP, P21 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 291 Co-crystals of CARmm Red domain with NADPH were obtained in 0.2 M ammonium tartrate dibasic, 20% PEG3350 (SG P21)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.54 α = 90 b = 58.95 β = 105.92 c = 135.56 γ = 90
Symmetry Space Group P 1 21 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 2016-02-17 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 1.74 130.36 100 0.08 1 11.7 3.7 156520
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 1.74 1.8 100 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MSO 1.74 130.36 148677 7843 99.71 0.18964 0.1884 0.21299 0.2226 RANDOM 41.321
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 0.08 1.37 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.715 r_dihedral_angle_4_deg 15.129 r_dihedral_angle_3_deg 11.93 r_long_range_B_refined 7.641 r_long_range_B_other 7.64 r_scangle_other 6.004 r_dihedral_angle_1_deg 5.779 r_scbond_it 3.983 r_scbond_other 3.982 r_mcangle_it 3.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.715 r_dihedral_angle_4_deg 15.129 r_dihedral_angle_3_deg 11.93 r_long_range_B_refined 7.641 r_long_range_B_other 7.64 r_scangle_other 6.004 r_dihedral_angle_1_deg 5.779 r_scbond_it 3.983 r_scbond_other 3.982 r_mcangle_it 3.572 r_mcangle_other 3.572 r_mcbond_it 2.674 r_mcbond_other 2.662 r_angle_refined_deg 1.407 r_angle_other_deg 1.269 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 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 10252 Nucleic Acid Atoms Solvent Atoms 1104 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing