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Crystal structure of RdxA from Helicobacter pyroli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICR pdb entry 1icr
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 25 % PEG 3350, 0.1 M Bis-Tris, 0.2 M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.44 α = 90 b = 49.44 β = 90 c = 304.48 γ = 90
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 MARMOSAIC 225 mm CCD 2010-02-19 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 325 mm CCD 2010-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2 2 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 ESRF BM14
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 2 76.12 99.7 0.145 8.1 5.5 48813 48813
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) 1,2 2 2.11 100 0.32 0.32 2.4 5.3 7115
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 1icr 2 76.12 48807 2511 99.6 0.1898 0.1881 0.1805 0.2203 0.2089 RANDOM 19.935
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] -0.36 -0.36 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.982 r_dihedral_angle_4_deg 16.34 r_dihedral_angle_3_deg 15.007 r_dihedral_angle_1_deg 4.915 r_scangle_it 0.933 r_angle_refined_deg 0.915 r_scbond_it 0.576 r_mcangle_it 0.509 r_mcbond_it 0.28 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.982 r_dihedral_angle_4_deg 16.34 r_dihedral_angle_3_deg 15.007 r_dihedral_angle_1_deg 4.915 r_scangle_it 0.933 r_angle_refined_deg 0.915 r_scbond_it 0.576 r_mcangle_it 0.509 r_mcbond_it 0.28 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5444 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 136
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction