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Crystal Structure of YhhW from Escherichia coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 PEG 400, sodium acetate, cadmium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.769 α = 90 b = 62.769 β = 90 c = 98.053 γ = 120
Symmetry Space Group P 32 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 SBC-3 2003-11-12 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98027 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.76 54.23 21480 19955 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.763 1.809 54.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 1.76 54.23 2 29187 19955 1074 92.9 0.20449 0.1972 0.2534 0.2503 0.2565 RANDOM 36.752
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] 6.212 1.916 6.212 -12.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.329 r_scangle_it 7.892 r_scbond_it 5.192 r_mcangle_it 3.422 r_angle_refined_deg 2.724 r_mcbond_it 1.998 r_angle_other_deg 1.19 r_symmetry_vdw_refined 0.357 r_symmetry_hbond_refined 0.357 r_symmetry_vdw_other 0.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.329 r_scangle_it 7.892 r_scbond_it 5.192 r_mcangle_it 3.422 r_angle_refined_deg 2.724 r_mcbond_it 1.998 r_angle_other_deg 1.19 r_symmetry_vdw_refined 0.357 r_symmetry_hbond_refined 0.357 r_symmetry_vdw_other 0.343 r_nbd_other 0.278 r_xyhbond_nbd_refined 0.272 r_nbd_refined 0.254 r_chiral_restr 0.171 r_metal_ion_refined 0.145 r_nbtor_other 0.106 r_bond_refined_d 0.038 r_gen_planes_refined 0.015 r_gen_planes_other 0.012 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_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 1870 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling SOLVE phasing CNS refinement DENZO data reduction