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Crystal structure of the Arabidopsis thaliana TOP2 oligopeptidase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 220 mM ammonium acetate and 20% (w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.44 72.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.74 α = 90 b = 168.74 β = 90 c = 175.59 γ = 120
Symmetry Space Group P 63 2 2
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 MIRRORS 2013-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3 50 98 0.086 13.4 4.5 30200 29598 3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 97.1 0.514 2.5 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MR THROUGHOUT 3 48.09 30200 28322 1404 94 0.207 0.207 0.207 0.2152 0.247 0.2423 RANDOM 55.6
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] 5.28 5.28 -10.57
RMS Deviations Key Refinement Restraint Deviation o_dihedral_angle_d 23 o_scangle_it 6.03 o_scbond_it 3.88 o_mcangle_it 3.85 o_mcbond_it 2.34 o_improper_angle_d 2.05 o_angle_deg 1.8 o_bond_d 0.018 o_bond_d_na o_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation o_dihedral_angle_d 23 o_scangle_it 6.03 o_scbond_it 3.88 o_mcangle_it 3.85 o_mcbond_it 2.34 o_improper_angle_d 2.05 o_angle_deg 1.8 o_bond_d 0.018 o_bond_d_na o_bond_d_prot o_angle_d o_angle_d_na o_angle_d_prot o_angle_deg_na o_angle_deg_prot o_dihedral_angle_d_na o_dihedral_angle_d_prot o_improper_angle_d_na o_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5517 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PRIME-X refinement DENZO data reduction SCALEPACK data scaling