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Crystal Structure of the DBL3x domain of the Plasmodium falcipurum VAR2CSA protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C6J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20-25% PEG 3350, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.785878 31.126314
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.67 α = 90 b = 84.2 β = 90 c = 86.49 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 118 CCD MARMOSAIC 225 mm CCD 2007-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.9 20 98.9 0.056 0.056 14.3 3.7 24118 23884 -6 -3 26.7
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) 1.9 2.02 94.4 0.627 0.627 2.2 3.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C6J 1.9 19.8 24118 23884 1880 98.9 0.223 0.223 0.2214 0.253 0.2506 RANDOM 43.4
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] 4.63 -1.78 -2.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 3.63 c_mcangle_it 3.19 c_scbond_it 2.38 c_mcbond_it 1.85 c_angle_deg 1.2 c_improper_angle_d 1.02 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.2 c_scangle_it 3.63 c_mcangle_it 3.19 c_scbond_it 2.38 c_mcbond_it 1.85 c_angle_deg 1.2 c_improper_angle_d 1.02 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose CNS refinement XDS data scaling XDS data reduction PHASER phasing