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Crystal structure of peroxidase from palm tree Chamaerops excelsa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HDL PDB ENTRY 3HDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.17 M AMMONIUM SULFATE, 0.085 M TRIS PH 8.0, 17% PEG MME 2K, 15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.11 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.18 α = 90 b = 100.65 β = 90 c = 132.31 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 2011-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 LNLS W01B-MX2
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 2.6 80.1 90.1 0.01 10.4 4.3 29525 3.7
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 2.6 2.69 91.8 0.56 3.7 4.3
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 PDB ENTRY 3HDL 2.6 80.11 25246 1369 90.14 0.21964 0.21816 0.2247 0.24585 0.2447 RANDOM 54.787
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] -4.23 10.61 -6.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.535 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 14.934 r_dihedral_angle_1_deg 5.849 r_mcangle_it 3.506 r_scbond_it 2.948 r_angle_other_deg 2.633 r_mcbond_other 2.211 r_mcbond_it 2.21 r_angle_refined_deg 1.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.535 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 14.934 r_dihedral_angle_1_deg 5.849 r_mcangle_it 3.506 r_scbond_it 2.948 r_angle_other_deg 2.633 r_mcbond_other 2.211 r_mcbond_it 2.21 r_angle_refined_deg 1.731 r_chiral_restr 0.083 r_gen_planes_other 0.023 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4461 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 314
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing