☰ Navigation Tabs
Crystal structure of CLEC-2 in complex with rhodocytin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C6U 2C6U and 2VRP experimental model PDB 2VRP 2C6U and 2VRP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 0.1M Hepes (pH 7.6), 0.2M L-proline, 10% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 55.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.851 α = 90 b = 117.072 β = 115.78 c = 152.238 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2014-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.98 100 99.7 0.099 16.9 3.6 41633 41508 44.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.983 3.05 99.9 0.458 2.9 3.6 2103
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 2C6U and 2VRP 2.98 37.56 39290 2089 98.01 0.28407 0.28192 0.2819 0.32492 0.322 RANDOM 60.923
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] 19.22 -0.7 21.86 -41.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.361 r_dihedral_angle_3_deg 14.214 r_dihedral_angle_1_deg 13.527 r_dihedral_angle_4_deg 9.819 r_long_range_B_refined 3.004 r_angle_refined_deg 1.619 r_mcangle_it 0.785 r_mcbond_it 0.417 r_scbond_it 0.214 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.361 r_dihedral_angle_3_deg 14.214 r_dihedral_angle_1_deg 13.527 r_dihedral_angle_4_deg 9.819 r_long_range_B_refined 3.004 r_angle_refined_deg 1.619 r_mcangle_it 0.785 r_mcbond_it 0.417 r_scbond_it 0.214 r_chiral_restr 0.129 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it r_scangle_other 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 12453 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling