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1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.15 α = 90 b = 55.64 β = 101.12 c = 63.33 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 ADSC QUANTUM 315 2007-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.8 44.99 97.3 0.067 0.067 15.3 3.7 49763 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) 1.8 1.89 96.4 0.428 0.428 3.2 3.8
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 1.8 38.9 49625 1994 100 0.179 0.178 0.1773 0.213 0.212 RANDOM 18.94
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.446 r_dihedral_angle_4_deg 16.111 r_dihedral_angle_3_deg 13.437 r_dihedral_angle_1_deg 6.957 r_scangle_it 3.099 r_mcangle_it 2.523 r_scbond_it 2.206 r_mcbond_it 1.787 r_angle_refined_deg 1.544 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.446 r_dihedral_angle_4_deg 16.111 r_dihedral_angle_3_deg 13.437 r_dihedral_angle_1_deg 6.957 r_scangle_it 3.099 r_mcangle_it 2.523 r_scbond_it 2.206 r_mcbond_it 1.787 r_angle_refined_deg 1.544 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_refined 0.144 r_symmetry_metal_ion_refined 0.105 r_chiral_restr 0.104 r_metal_ion_refined 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4012 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling PHENIX phasing