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Crystal structure of Emp47p carbohydrate recognition domain (CRD), orthorhombic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A6Z PDB ENTRY 2A6Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 283 PEG4000, Ammonium acetate, Sodium cacodylate, Calcuim chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.2 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.59 α = 90 b = 129.62 β = 90 c = 170.45 γ = 90
Symmetry Space Group P 21 21 21
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 2004-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.9779 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 2.7 50 87.7 0.105 8.7 4.1 25245 22129 54.4
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) 2.7 2.8 90.9 0.42 4.8 4 2242
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A6Z 2.7 20 20823 20823 1125 87.8 0.201 0.201 0.198 0.258 0.2277 RANDOM 31.969
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] -0.41 0.23 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.554 r_scangle_it 2.228 r_angle_refined_deg 1.332 r_scbond_it 1.268 r_mcangle_it 1.265 r_angle_other_deg 0.826 r_mcbond_it 0.678 r_nbd_other 0.226 r_symmetry_vdw_other 0.223 r_nbd_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.554 r_scangle_it 2.228 r_angle_refined_deg 1.332 r_scbond_it 1.268 r_mcangle_it 1.265 r_angle_other_deg 0.826 r_mcbond_it 0.678 r_nbd_other 0.226 r_symmetry_vdw_other 0.223 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.179 r_symmetry_vdw_refined 0.146 r_nbtor_other 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 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 6878 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing