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Crystal structure of the periplasmic domain of the Escherichia Coli YIDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.1 295 0.1 M glycine, 0.2 M ammonium sulfate, 13% PEG3350, pH 3.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.99 69.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.127 α = 90 b = 126.127 β = 90 c = 288.459 γ = 90
Symmetry Space Group I 41 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 ADSC QUANTUM 315 mirrors 2007-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9794 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 50 99.1 0.079 0.079 44.7 13.8 40327 2 2
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 2.5 2.6 92 0.379 0.379 4 9.7 3687
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.5 50 38278 2021 98.93 0.2135 0.21165 0.2027 0.24897 0.2365 RANDOM 34.447
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] 2.13 2.13 -4.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.488 r_dihedral_angle_3_deg 18.498 r_dihedral_angle_4_deg 17.166 r_dihedral_angle_1_deg 6.994 r_scangle_it 2.62 r_scbond_it 1.819 r_angle_refined_deg 1.515 r_mcangle_it 1.018 r_mcbond_it 0.665 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.488 r_dihedral_angle_3_deg 18.498 r_dihedral_angle_4_deg 17.166 r_dihedral_angle_1_deg 6.994 r_scangle_it 2.62 r_scbond_it 1.819 r_angle_refined_deg 1.515 r_mcangle_it 1.018 r_mcbond_it 0.665 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4291 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SHELXS phasing