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Crystal structure of human CLEC-2 (CLEC1B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other COMPOSITE MODEL - SEE REMARKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 20% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000 0.1M BIS-TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 1.81 31.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.064 α = 90 b = 55.065 β = 90 c = 56.165 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 CCD MIRRORS 2005-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 1.44 50 88 0.04 49.02 11.4 20396 -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 1.44 1.49 24.4 0.11 10.13 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 COMPOSITE MODEL - SEE REMARKS 1.6 39.31 14114 762 99.8 0.161 0.159 0.1572 0.198 0.1975 RANDOM 13.02
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] 0.66 -0.43 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.264 r_dihedral_angle_4_deg 18.92 r_dihedral_angle_3_deg 14.222 r_dihedral_angle_1_deg 6.163 r_scangle_it 3.131 r_scbond_it 2.168 r_mcangle_it 1.191 r_angle_refined_deg 1.187 r_mcbond_it 0.779 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.264 r_dihedral_angle_4_deg 18.92 r_dihedral_angle_3_deg 14.222 r_dihedral_angle_1_deg 6.163 r_scangle_it 3.131 r_scbond_it 2.168 r_mcangle_it 1.191 r_angle_refined_deg 1.187 r_mcbond_it 0.779 r_nbtor_refined 0.31 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.165 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1021 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CaspR phasing