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Crystal structure of the FK506 binding domain of Plasmodium vivax FKBP35 in complex with FK506
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VN1 PDB Entry 2VN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277 100mM BICINE pH 9.0, 2.4M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.9 α = 90 b = 40.9 β = 109.5 c = 56.9 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 93 IMAGE PLATE MAR scanner 345 mm plate mirrors 2009-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.66 21.22 0.029 0.029 30.4 4.9 28738 28288 2354.8 21
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) 1.66 1.75 0.15 0.15 8.2 4.6 3782
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 PDB Entry 2VN1 1.67 21.22 26851 1425 99.57 0.19009 0.1878 0.1802 0.23277 0.2211 RANDOM 20.859
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 r_dihedral_angle_2_deg 37.333 r_dihedral_angle_4_deg 20.665 r_dihedral_angle_3_deg 16.263 r_dihedral_angle_1_deg 6.217 r_scangle_it 4.214 r_scbond_it 2.572 r_mcangle_it 1.716 r_angle_refined_deg 1.502 r_mcbond_it 0.947 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.333 r_dihedral_angle_4_deg 20.665 r_dihedral_angle_3_deg 16.263 r_dihedral_angle_1_deg 6.217 r_scangle_it 4.214 r_scbond_it 2.572 r_mcangle_it 1.716 r_angle_refined_deg 1.502 r_mcbond_it 0.947 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1888 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 57
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling