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Crystal structure of NADP-binding form of malonyl-CoA reductase C-domain from Chloroflexus aurantiacus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I6Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.1 M ammonium tartrate, 0.1 M Tris-Cl
Crystal Properties Matthews coefficient Solvent content 3.02 59.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.675 α = 90 b = 139.644 β = 97.71 c = 73.565 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 CCD ADSC QUANTUM 270 2016-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 50 98.8 0.064 12.9 2.1 67574
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 98.1 0.232 2.1
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 8I6Z 1.9 26.54 63699 3556 99.51 0.15425 0.15229 0.1659 0.19129 0.1973 RANDOM 26.733
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] 1.34 -0.86 -0.57 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.787 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_3_deg 13.334 r_long_range_B_refined 7.416 r_long_range_B_other 7.344 r_dihedral_angle_1_deg 6.22 r_scangle_other 5.934 r_scbond_it 3.964 r_scbond_other 3.964 r_mcangle_it 3.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.787 r_dihedral_angle_4_deg 13.66 r_dihedral_angle_3_deg 13.334 r_long_range_B_refined 7.416 r_long_range_B_other 7.344 r_dihedral_angle_1_deg 6.22 r_scangle_other 5.934 r_scbond_it 3.964 r_scbond_other 3.964 r_mcangle_it 3.186 r_mcangle_other 3.186 r_mcbond_it 2.477 r_mcbond_other 2.476 r_angle_refined_deg 1.728 r_angle_other_deg 1.476 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5080 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing