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Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 2
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 7.8 283 PEG3350, Potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2 36.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.62 α = 90 b = 65.21 β = 96.66 c = 72.46 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 2004-01-16 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 1.05 50 98.5 0.065 8.9 3.6 178928 176286 5.5
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) 1.05 1.09 85.6 0.38 2.3 2.6 15231
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 (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 1.1 10 147540 147540 7802 95 0.135 0.135 0.173 0.1197 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 21 4165
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.096 s_approx_iso_adps 0.091 s_zero_chiral_vol 0.085 s_similar_adp_cmpnt 0.046 s_from_restr_planes 0.0315 s_angle_d 0.031 s_anti_bump_dis_restr 0.028 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3553 Nucleic Acid Atoms Solvent Atoms 643 Heterogen Atoms 24
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing