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Crystal structure of Plasmodium falciparum diadenosine triphosphate hydrolase in complex with Cyclomarin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 uL of protein-inhibitor solution (11 mg/ml PFAp3Aase, 50 mM TRIS pH 8, 150 mM NaCl, 5% glycerol and 1 mM TCEP, 1mM cyclomarin A) was mixed with 0.2 uL reservoir solution (100 mM HEPES pH 7.5, 30% Iso-propanol, 200 mM Magnesium chloride hexahydrate) and equilibrated against 80 uL reservoir solution.
Crystal Properties Matthews coefficient Solvent content 1.71 27.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.953 α = 90 b = 45.953 β = 90 c = 138.44 γ = 120
Symmetry Space Group P 32 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 100 PIXEL DECTRIS PILATUS 6M 2014-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99997 SLS X10SA
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 1.65 17.5 98.5 0.051 20.3 8 20919 26.19
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 1.65 1.69 100 0.75 2.4 7.2
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 2FHI 1.65 17.5 20891 1044 98.49 0.1967 0.1953 0.1985 0.2232 0.2199 RANDOM 31.74
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] -4.1758 -4.1758 8.3517
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.97 t_omega_torsion 3.35 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.97 t_omega_torsion 3.35 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1235 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 1
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing