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Disproportionating enzyme 1 from Arabidopsis - apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 microliter of 9% PEG2000 MME in 0.1 M HEPES-NaOH, pH 8.0 was added to 1 microliter of protein at a concentration of 10 mg/ml in 20 mM HEPES-NaOH, pH 7.5, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.65 α = 64.97 b = 74.22 β = 69.48 c = 79.7 γ = 66.02
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2011-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 2.126 70.515 92.6 0.084 0.106 0.063 6.7 2.7 68185 68185 35.7
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 2.13 2.24 84.4 0.541 0.541 0.404 1.4 2.6 9066
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 1X1N 2.13 57.78 64404 3459 92.73 0.1884 0.1868 0.1956 0.2182 0.2249 RANDOM 42.1
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] 1.03 1.68 0.43 -0.51 -1.64 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.256 r_dihedral_angle_4_deg 17.945 r_dihedral_angle_3_deg 13.326 r_dihedral_angle_1_deg 5.868 r_mcangle_it 1.944 r_angle_refined_deg 1.401 r_mcbond_it 1.219 r_mcbond_other 1.216 r_angle_other_deg 0.934 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.256 r_dihedral_angle_4_deg 17.945 r_dihedral_angle_3_deg 13.326 r_dihedral_angle_1_deg 5.868 r_mcangle_it 1.944 r_angle_refined_deg 1.401 r_mcbond_it 1.219 r_mcbond_other 1.216 r_angle_other_deg 0.934 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8009 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 64
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing XDS data reduction