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Crystal structure of the erythrocyte-binding domain from Plasmodium vivax reticulocyte-binding protein 2b (PvRBP2b)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z8N PDB ENTRY 4Z8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 22% W/V PEG3350, 200 MM POTASSIUM
THIOCYANATE, 100 MM BIS-TRIS-HCL, PH 7.5, VAPOR DIFFUSION,
HANGING DROP, TEMPERATURE 295K
Crystal Properties Matthews coefficient Solvent content 3.3 62.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.5 α = 90 b = 124.2 β = 97.75 c = 65.31 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2014-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.71 34.87 99.4 0.111 10 7.4 100494
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 1.71 1.74 98.8 1.711 1.2 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB ENTRY 4Z8N 1.71 34.17 1.36 100440 1006 99.3 0.168 0.168 0.1724 0.188 0.1883 Random selection 35.45
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.078 f_angle_d 1.321 f_chiral_restr 0.068 f_bond_d 0.014 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5100 Nucleic Acid Atoms Solvent Atoms 824 Heterogen Atoms 23
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling PHASER phasing PHENIX refinement