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Crystal structure of the APO Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 KDO1 : 9.3 mg/ml in 0.2 M NaCl, .001 M DTT, 0.05M Tris-HCl, pH 8
Precipitant : 18% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate
Soaking/cryo : 20% PEG3350, 0.15 M Tris pH 7.5, 0.3 M Na Acetate, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.65 α = 107.85 b = 68.09 β = 102.84 c = 110.22 γ = 93.23
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 2014-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 50 98.5 0.0117 0.997 10.24 4.65 117676 29.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 95.6 0.668 1.31 3.45
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 1.9 38 117663 5883 98.6 0.178 0.177 0.1787 0.203 0.2042 RANDOM 37.56
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] -2.862 0.4597 -0.1197 -4.8629 2.7835 7.725
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.98 t_omega_torsion 3.29 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.98 t_omega_torsion 3.29 t_angle_deg 0.97 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10076 Nucleic Acid Atoms Solvent Atoms 1343 Heterogen Atoms 16
Software Software Software Name Purpose BUSTER refinement Coot model building XDS data reduction XSCALE data scaling