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Alpha-ketoisovalerate decarboxylase (Kivd) from Synechocystis sp. PCC 6803 with substitution S286T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298.15 16 - 17.8 % (w/v) PEG6000 or PEG3350, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.21 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.465 α = 90 b = 81.731 β = 105.52 c = 124.981 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 EIGER2 XE 16M 2022-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.79 40 99.7 0.11 0.12 0.999 12 7 53028
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.81 99.43 0.026 0.3 0.9 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.79 40 50371 2656 99.7 0.19156 0.18932 0.1891 0.23391 0.2338 RANDOM 86.03
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] -0.57 0.89 -1.67 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.889 r_long_range_B_refined 7.515 r_dihedral_angle_2_deg 6.644 r_dihedral_angle_1_deg 6.301 r_mcangle_it 4.76 r_scbond_it 3.283 r_mcbond_it 2.976 r_angle_refined_deg 1.479 r_chiral_restr 0.11 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.889 r_long_range_B_refined 7.515 r_dihedral_angle_2_deg 6.644 r_dihedral_angle_1_deg 6.301 r_mcangle_it 4.76 r_scbond_it 3.283 r_mcbond_it 2.976 r_angle_refined_deg 1.479 r_chiral_restr 0.11 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 16304 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing