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Crystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in complex with alpha-KG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 20 mM ammonium acetate, 24% v/v polyethylene glycol 400, 0.1 M sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.63 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.115 α = 90 b = 127.191 β = 90 c = 138.759 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX300-HS 2021-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
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 1.67 30 99.9 0.055 24.05 4.5 95108
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 1.67 1.73 100 0.76 0.757 2.02 4.4
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 2WBO 1.67 27.67 85445 4533 94.35 0.1788 0.178 0.1874 0.1936 0.2018 RANDOM 16.668
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] -0.16 -0.15 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.106 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_3_deg 12.434 r_dihedral_angle_1_deg 6.928 r_angle_other_deg 1.324 r_angle_refined_deg 1.279 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.106 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_3_deg 12.434 r_dihedral_angle_1_deg 6.928 r_angle_other_deg 1.324 r_angle_refined_deg 1.279 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5228 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 31
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing