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Crystal structure of chloroplastic ascorbate peroxidase from tobacco plants and structural insights for its instability
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1APX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG 4000, Tris-HCl, Magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.188 α = 90 b = 76.79 β = 90 c = 98.776 γ = 90
Symmetry Space Group P 21 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 CCD ADSC QUANTUM 4 2001-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 Photon Factory BL-18B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 8 99.8 0.065 0.065 8.1 6.4 38117 38108 13.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.69 99.8 0.239 0.239 3.1 6 5467
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1APX 1.6 7.99 37822 37796 3794 99.9 0.191 0.191 0.191 0.1848 0.222 0.2166 RANDOM 15.1
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] 1.25 0.74 -1.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 6.45 c_scbond_it 4.81 c_mcangle_it 2.72 c_mcbond_it 2.17 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 6.45 c_scbond_it 4.81 c_mcangle_it 2.72 c_mcbond_it 2.17 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2138 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 45
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CNS refinement CCP4 data scaling CNS phasing