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IspF (Plasmodium falciparum) unliganded structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C81 PDB ENTRY 4C81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. PFISPF SAMPLE IN 100 MM KCL, 100 MM L-ARGININE, 2 MM MGCL2, 50 MM CHES, PH 9.5; WAS CONCENTRATED TO 6 MG/ML, AND HAD FOSMIDOMYCIN ADDED (20 MM FINAL CONCENTRATION). CRYSTALS WERE OBTAINED BY MIXING 2 MICROLITES OF PROTEIN WITH 2 MICROLITRES OF RESERVOIR SOLUTION AT 20 DEGREES C. RESERVOIR SOLUTION: 1.8-2.5 M (NH4)2SO4, 5MM ZNCL2, 100 MM BIS-TRIS, PH 5.5. SATURATED SUCROSE WAS USED AS A CRYO-PROTECTANT DURING COLLECTION.
Crystal Properties Matthews coefficient Solvent content 3.4 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.223 α = 90 b = 84.223 β = 90 c = 102.451 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV PLUS PLUS 2010-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2 29.71 98.6 0.09 5.3 2.3 18068 2 32
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 2 2.11 97 0.48 2 2.2
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 4C81 2 29.72 17023 1044 98.58 0.19689 0.19441 0.1926 0.22629 0.2259 RANDOM 37.598
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] -0.26 -0.13 -0.26 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.073 r_dihedral_angle_3_deg 19.187 r_dihedral_angle_4_deg 10.28 r_dihedral_angle_1_deg 6.662 r_angle_refined_deg 2.087 r_chiral_restr 0.152 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.073 r_dihedral_angle_3_deg 19.187 r_dihedral_angle_4_deg 10.28 r_dihedral_angle_1_deg 6.662 r_angle_refined_deg 2.087 r_chiral_restr 0.152 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1213 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing