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Structure of a chondroitin sulphate binding DBL3X from a var2csa encoded PfEMP1 protein
Crystallization Crystal Properties Matthews coefficient Solvent content 2.03 39.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.482 α = 90 b = 86.889 β = 90 c = 92.898 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 MAR CCD 165 mm 2007-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.2 31.73 97.2 0.069 0.069 14.6 3.4 17198 2 2
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 2.32 92.8 0.448 0.448 2.6 3.4 1997
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 SAD THROUGHOUT 2.2 31.73 2 16289 16289 869 96.99 0.2389 0.22937 0.22596 0.29112 0.2725 RANDOM 36.262
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] 0.25 -0.13 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.36 r_dihedral_angle_3_deg 15.637 r_dihedral_angle_4_deg 14.143 r_dihedral_angle_1_deg 5.45 r_scangle_it 1.707 r_scbond_it 1.032 r_mcangle_it 1.027 r_angle_refined_deg 0.996 r_mcbond_it 0.58 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.36 r_dihedral_angle_3_deg 15.637 r_dihedral_angle_4_deg 14.143 r_dihedral_angle_1_deg 5.45 r_scangle_it 1.707 r_scbond_it 1.032 r_mcangle_it 1.027 r_angle_refined_deg 0.996 r_mcbond_it 0.58 r_nbtor_refined 0.296 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2659 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling SHARP phasing