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Crystal structure of IpgC in complex with an IpaB peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GYZ PDB ENTRY 3GYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1M ADA, 1M ammonium sulfate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.34 63.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.72 α = 90 b = 113.72 β = 90 c = 76.37 γ = 120
Symmetry Space Group P 31 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 2008-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 2.65 35.6 92.6 0.069 26.38 17.3 16875 15633 -3 83.627
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) 2.65 2.8 90.4 0.84 3.4 13.6 2288
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 3GYZ 2.65 35.6 16864 15633 782 92.7 0.235 0.233 0.2257 0.273 0.2596 RANDOM 79.28
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] 2.47 1.23 2.47 -3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.774 r_dihedral_angle_4_deg 21.732 r_dihedral_angle_3_deg 19.396 r_dihedral_angle_1_deg 5.499 r_scangle_it 4.279 r_scbond_it 2.528 r_angle_refined_deg 1.894 r_mcangle_it 1.848 r_mcbond_it 0.945 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.774 r_dihedral_angle_4_deg 21.732 r_dihedral_angle_3_deg 19.396 r_dihedral_angle_1_deg 5.499 r_scangle_it 4.279 r_scbond_it 2.528 r_angle_refined_deg 1.894 r_mcangle_it 1.848 r_mcbond_it 0.945 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 17
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction