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Disproportionating enzyme 1 from Arabidopsis - acarviostatin soak
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 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.83 α = 64.59 b = 74.13 β = 69.76 c = 79.73 γ = 66.57
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 2013-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9790 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.53 40.95 95.9 0.122 0.085 0.984 5.7 2.9 42064 31.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.6 96.4 0.515 0.358 0.701 1.9 2.9 3104
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 2.53 40.95 39812 2181 95.73 0.2094 0.2072 0.211 0.2486 0.2503 RANDOM 42.6
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] -0.27 0.8 0.66 -0.31 -1.2 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.202 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_1_deg 6.184 r_mcangle_it 1.543 r_angle_refined_deg 1.439 r_angle_other_deg 1.1 r_mcbond_it 0.916 r_mcbond_other 0.91 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.202 r_dihedral_angle_3_deg 15.668 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_1_deg 6.184 r_mcangle_it 1.543 r_angle_refined_deg 1.439 r_angle_other_deg 1.1 r_mcbond_it 0.916 r_mcbond_other 0.91 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7992 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction