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Crystal structure resolution of Plasmodium falciparum FK506 binding domain (FKBP35) in complex with Rapamycin at 1.4A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1M MMT, 25% PEG1500, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.476 α = 90 b = 50.157 β = 90 c = 57.813 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 PIXEL PSI PILATUS 6M 2014-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 1.4 50.15 99.5 28931 28857 1.8 12
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 2VN1 1.4 37.89 28857 28809 1466 99.33 0.1494 0.1475 0.1574 0.1871 0.1937 RANDOM 22.098
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 -0.65 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_sphericity_free 24.359 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 13.267 r_dihedral_angle_1_deg 6.265 r_sphericity_bonded 5.835 r_rigid_bond_restr 4.501 r_angle_other_deg 2.396 r_mcangle_it 1.935 r_mcbond_it 1.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_sphericity_free 24.359 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 13.267 r_dihedral_angle_1_deg 6.265 r_sphericity_bonded 5.835 r_rigid_bond_restr 4.501 r_angle_other_deg 2.396 r_mcangle_it 1.935 r_mcbond_it 1.515 r_mcbond_other 1.496 r_angle_refined_deg 1.342 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 986 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DNA data collection MOSFLM data reduction SCALA data scaling MOLREP phasing