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Crystal structure of Xylella fastidiosa organic peroxide resistance protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N2F PDB ENTRY 1N2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293 Peg 4000, Tris-HCl, 0,29mM t-BOOH, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.19 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.697 α = 90 b = 91.697 β = 90 c = 157.178 γ = 120
Symmetry Space Group P 65 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 110 CCD MARRESEARCH mirrors 2004-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.453 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 79.31 0.061 10.3 7.4 15924
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 0.267 2.8 7.1
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 (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 1N2F 2.4 79.31 15858 15130 794 99.9 0.19491 0.19232 0.1904 0.24371 0.2362 RANDOM 27.664
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] -0.74 -0.37 -0.74 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.148 r_dihedral_angle_4_deg 15.972 r_dihedral_angle_3_deg 15.63 r_dihedral_angle_1_deg 6.121 r_scangle_it 3.228 r_scbond_it 1.993 r_angle_refined_deg 1.739 r_mcangle_it 1.395 r_mcbond_it 0.777 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.148 r_dihedral_angle_4_deg 15.972 r_dihedral_angle_3_deg 15.63 r_dihedral_angle_1_deg 6.121 r_scangle_it 3.228 r_scbond_it 1.993 r_angle_refined_deg 1.739 r_mcangle_it 1.395 r_mcbond_it 0.777 r_nbtor_refined 0.311 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.148 r_symmetry_vdw_refined 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2052 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MAR345 data collection CCP4 data scaling AMoRE phasing