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Structure of a chondroitin sulphate binding DBL3X domain from a var2csa encoded PfEMP1 protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 25% PEG 4K, 20mM HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.576 α = 90 b = 86.99 β = 90 c = 92.659 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 1 2007-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.06 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 62.99 97.7 0.083 0.083 11.6 3.8 30158 2 2 27.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.348 0.348 5.4 7.2 11894
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 2 46.32 2 2 22216 1202 99.97 0.22486 0.22244 0.27081 0.2721 RANDOM 33.29
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] 0.17 -0.2 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_4_deg 12.828 r_dihedral_angle_1_deg 7.904 r_scangle_it 2.904 r_scbond_it 1.813 r_mcangle_it 1.563 r_angle_refined_deg 1.137 r_mcbond_it 0.922 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.306 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_4_deg 12.828 r_dihedral_angle_1_deg 7.904 r_scangle_it 2.904 r_scbond_it 1.813 r_mcangle_it 1.563 r_angle_refined_deg 1.137 r_mcbond_it 0.922 r_nbtor_refined 0.299 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.167 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2732 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling SHARP phasing