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Crystal structure of Emp46p carbohydrate recognition domain (CRD), potassium-bound form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 PEG3350, Potassium fluoride, HEPES, Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.2 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.32 α = 90 b = 55.89 β = 108.28 c = 77.47 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 100 CCD ADSC QUANTUM 4 2004-01-21 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4 2003-12-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0000 Photon Factory BL-18B 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.9700, 0.9790, 0.9794 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.52 50 99.6 0.039 13.3 3.7 68062 67798 18.7
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) 1.52 1.57 99.9 0.328 3.6 3.5 6716
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 MAD THROUGHOUT 1.52 20 64233 64233 3438 99.6 0.191 0.191 0.189 0.1999 0.218 0.2251 RANDOM 17.93
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] -0.08 -0.47 0.15 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.25 r_scangle_it 3.424 r_scbond_it 2.081 r_mcangle_it 1.56 r_angle_refined_deg 1.404 r_angle_other_deg 1.266 r_mcbond_it 0.853 r_symmetry_vdw_other 0.263 r_nbd_other 0.25 r_symmetry_vdw_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.25 r_scangle_it 3.424 r_scbond_it 2.081 r_mcangle_it 1.56 r_angle_refined_deg 1.404 r_angle_other_deg 1.266 r_mcbond_it 0.853 r_symmetry_vdw_other 0.263 r_nbd_other 0.25 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.222 r_metal_ion_refined 0.149 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3484 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing