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Crystal structure of Emp46p carbohydrate recognition domain (CRD), metal-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A6V PDB ENTRY 2A6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 PEG1000, HEPES, Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.93 α = 90 b = 55.78 β = 107.99 c = 77.66 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 2004-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 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 1.75 50 99.8 0.045 17 3.8 45402 45303 26.3
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) 1.75 1.81 100 0.355 4 3.7 4517
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A6V 1.75 20 42874 42874 2272 99.8 0.211 0.211 0.21 0.2168 0.237 0.2441 RANDOM 27.72
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 0.29 -0.55 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.928 r_scangle_it 3.307 r_scbond_it 2.012 r_mcangle_it 1.797 r_angle_refined_deg 1.405 r_angle_other_deg 1.061 r_mcbond_it 0.992 r_nbd_other 0.241 r_symmetry_vdw_other 0.225 r_nbd_refined 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.928 r_scangle_it 3.307 r_scbond_it 2.012 r_mcangle_it 1.797 r_angle_refined_deg 1.405 r_angle_other_deg 1.061 r_mcbond_it 0.992 r_nbd_other 0.241 r_symmetry_vdw_other 0.225 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.143 r_chiral_restr 0.087 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_refined r_metal_ion_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 3487 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing