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Crystal Structure of oxidoreductase DsbA from Xylella fastidiosa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 30% PEG 4000, 0.1M acetate chloride, Guanidine Hydrochloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.117 α = 90 b = 41.722 β = 95.87 c = 79.807 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2005-01-26 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2006-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.4310 LNLS D03B-MX1 2 SYNCHROTRON NSLS BEAMLINE X26C 0.9795 NSLS X26C
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 1.9 50 99.7 0.074 7.3 3.5 52300 52143 2 2 21.8
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) 1.9 1.97 98.3 0.479 2.9 5052
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.9 50 2 2 52367 52137 2657 99.56 0.204 0.185 0.183 0.1826 0.224 0.222 RANDOM 24.959
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] -0.43 -0.36 1.09 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.27 r_dihedral_angle_4_deg 20.641 r_dihedral_angle_3_deg 14.155 r_dihedral_angle_1_deg 5.475 r_scangle_it 3.408 r_scbond_it 2.098 r_angle_refined_deg 1.288 r_mcangle_it 1.116 r_mcbond_it 0.688 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.27 r_dihedral_angle_4_deg 20.641 r_dihedral_angle_3_deg 14.155 r_dihedral_angle_1_deg 5.475 r_scangle_it 3.408 r_scbond_it 2.098 r_angle_refined_deg 1.288 r_mcangle_it 1.116 r_mcbond_it 0.688 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4489 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling