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Apo structure of KARI from Ignisphaera aggregans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XDZ
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 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.065 α = 90 b = 67.482 β = 90 c = 112.35 γ = 90
Symmetry Space Group P 2 21 21
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 2014-03-06 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 1.391 57.849 97.1 0.038 0.044 0.022 13.6 3.6 71148 71148
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.391 1.47 87.5 1.689 1.079 0.5 3 8928
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 4XDZ 1.391 57.849 68932 3474 96.77 0.1787 0.1757 0.2355 0.2416 RANDOM 31.033
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] 0.67 0.65 -1.32
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.868 r_sphericity_bonded 17.647 r_rigid_bond_restr 5.97 r_mcangle_it 4.863 r_mcbond_other 4.187 r_mcbond_it 4.186 r_angle_refined_deg 1.926 r_angle_other_deg 0.938 r_chiral_restr 0.124 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.868 r_sphericity_bonded 17.647 r_rigid_bond_restr 5.97 r_mcangle_it 4.863 r_mcbond_other 4.187 r_mcbond_it 4.186 r_angle_refined_deg 1.926 r_angle_other_deg 0.938 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing