☰ Navigation Tabs
Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant
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 PEG3350, Potassium fluoride, HEPES, Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.2 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.24 α = 90 b = 56.03 β = 108.64 c = 77.67 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 315 2004-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.55 50 98.1 0.053 15.6 3.6 64255 63029 24.6
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) 1.55 1.61 97.3 0.381 2.8 3.3 6196
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 1.55 20 59756 59756 3193 98.1 0.203 0.203 0.202 0.2078 0.235 0.2329 RANDOM 23.54
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] -0.53 -0.81 0.06 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.25 r_scangle_it 3.405 r_scbond_it 2.109 r_mcangle_it 1.635 r_angle_refined_deg 1.398 r_angle_other_deg 1.065 r_mcbond_it 0.901 r_symmetry_vdw_refined 0.375 r_symmetry_vdw_other 0.267 r_nbd_other 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.25 r_scangle_it 3.405 r_scbond_it 2.109 r_mcangle_it 1.635 r_angle_refined_deg 1.398 r_angle_other_deg 1.065 r_mcbond_it 0.901 r_symmetry_vdw_refined 0.375 r_symmetry_vdw_other 0.267 r_nbd_other 0.247 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.168 r_metal_ion_refined 0.166 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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_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 3494 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing