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Crystal structure of the periplasmic domain of CadC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.5 M ammonium sulfate, 7% (v/v) 2-propanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 49.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.898 α = 90 b = 83.898 β = 90 c = 199.09 γ = 120
Symmetry Space Group P 61 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 100 CCD MARMOSAIC 225 mm CCD mirrors 2008-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.8 72.66 100 0.085 14.3 39362 39362 2 2
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) 1.8 1.9 100 0.274 9.5 15.1 5617
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 3LYA 1.8 72.66 39276 1973 99.93 0.192 0.192 0.191 0.1846 0.218 0.2109 RANDOM 17.041
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] 0.45 0.23 0.45 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.522 r_dihedral_angle_4_deg 14.982 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 4.816 r_scangle_it 3.996 r_scbond_it 2.375 r_mcangle_it 1.607 r_angle_refined_deg 1.217 r_mcbond_it 0.838 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.522 r_dihedral_angle_4_deg 14.982 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 4.816 r_scangle_it 3.996 r_scbond_it 2.375 r_mcangle_it 1.607 r_angle_refined_deg 1.217 r_mcbond_it 0.838 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2556 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection