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Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LF4 PDB entry 1LF4
Crystallization Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.659 α = 90 b = 39.567 β = 105.54 c = 90.532 γ = 90
Symmetry Space Group P 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.92 NSLS X9B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 19.8 29457
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1LF4 1.9 19.8 28753 28457 1443 99 0.212 0.2118 0.222 0.2216 Random
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] -5 8.7 -3.6 1.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.1 c_angle_deg 1.4 c_improper_angle_d 0.8 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2568 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms
Software Software Software Name Purpose CNS refinement