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Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KQX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 0.1 M bis-tris pH 6, 22% polyethylene glycol monomethylether 5000
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.579 α = 90 b = 90.753 β = 100.25 c = 69.525 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 2014-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.15 68.415 95 0.079 0.096 0.054 6.9 3 236179
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.21 82.4 0.87 0.87 0.643 0.9 2.5 28356
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 4KQX 1.15 68.415 224341 11215 94.87 0.1582 0.1565 0.1561 0.1895 0.1887 RANDOM 13.086
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] -0.23 -0.01 0.1 0.13
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 24.013 r_rigid_bond_restr 7.914 r_sphericity_bonded 7.468 r_angle_refined_deg 2.461 r_mcangle_it 1.86 r_mcbond_it 1.565 r_mcbond_other 1.561 r_angle_other_deg 1.034 r_chiral_restr 0.287 r_bond_refined_d 0.024
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 24.013 r_rigid_bond_restr 7.914 r_sphericity_bonded 7.468 r_angle_refined_deg 2.461 r_mcangle_it 1.86 r_mcbond_it 1.565 r_mcbond_other 1.561 r_angle_other_deg 1.034 r_chiral_restr 0.287 r_bond_refined_d 0.024 r_gen_planes_refined 0.016 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5139 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing