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Crystal structure of metalloprotein yiiX from Escherichia coli O157:H7, DUF1105
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 100 mM Hepes pH 7.0, 30% Jeffamine ED-2001, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.8 56.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.345 α = 90 b = 152.594 β = 92.67 c = 48.74 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MAR CCD 165 mm 2006-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 20 93.2 0.111 0.122 12.1 5.1 40462 40462 19.6
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 1.8 1.9 79.9 0.709 0.813 2.3 3.7 5019
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.8 20 40348 40348 1999 92.84 0.18117 0.18117 0.17861 0.1845 0.23103 0.238 RANDOM 24.363
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] -1.61 -0.11 0.07 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 13.285 r_dihedral_angle_1_deg 6.01 r_scangle_it 4.344 r_scbond_it 2.72 r_mcangle_it 1.552 r_angle_refined_deg 1.421 r_mcbond_it 1.022 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 13.285 r_dihedral_angle_1_deg 6.01 r_scangle_it 4.344 r_scbond_it 2.72 r_mcangle_it 1.552 r_angle_refined_deg 1.421 r_mcbond_it 1.022 r_nbtor_refined 0.31 r_xyhbond_nbd_refined 0.222 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.145 r_metal_ion_refined 0.101 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2937 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing