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Crystal Structure of Xylella fastidiosa PrxQ C47S Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E2Y PDB entry 1E2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Crystallized in presence of 10 mM DTT. The optimal condition was obtained with the reservoir solution comprising 0.1 M Hepes-NaOH (pH 7.5) and 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.973 α = 90 b = 39.743 β = 90 c = 99.836 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 110 CCD MARMOSAIC 225 mm CCD mirrors 2008-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.549 LNLS W01B-MX2
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 1.6 30.7 98.01 0.063 6.3 13.3 20832 19697 2 6.1
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) 1.6 1.64 95.46 0.36 6.1 13.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1E2Y 1.6 27.83 19695 1065 98.02 0.19836 0.19579 0.24669 0.2291 RANDOM 20.433
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] -0.19 0.38 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.548 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_4_deg 11.404 r_dihedral_angle_1_deg 7.065 r_scangle_it 5.313 r_scbond_it 3.616 r_mcangle_it 2.445 r_angle_refined_deg 2.354 r_mcbond_it 1.512 r_chiral_restr 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.548 r_dihedral_angle_3_deg 13.787 r_dihedral_angle_4_deg 11.404 r_dihedral_angle_1_deg 7.065 r_scangle_it 5.313 r_scbond_it 3.616 r_mcangle_it 2.445 r_angle_refined_deg 2.354 r_mcbond_it 1.512 r_chiral_restr 0.182 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1244 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling