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Crystal Structure of PF10_0123, a GMP Synthetase from Plasmodium Falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 16% PEG3350
0.2 M CaAcet
5 mM MgCl2
2.5 mM XMP
2 mM TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.158 α = 103.07 b = 67.76 β = 99.36 c = 99.825 γ = 94.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2011-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 .91790 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 35 99 0.094 22 3.9 28348 74.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 98.9 0.76 2.35 3.9 1428
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 (All) 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 1GPM 2.72 30 28992 28331 1449 97.72 0.2605 0.2605 0.2585 0.2557 0.2964 0.2948 RANDOM 57.1479
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] 0.38 0.19 -0.39 2.78 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.175 r_dihedral_angle_3_deg 14.53 r_dihedral_angle_4_deg 11.772 r_dihedral_angle_1_deg 3.87 r_angle_refined_deg 0.854 r_scangle_it 0.663 r_mcangle_it 0.432 r_scbond_it 0.374 r_mcbond_it 0.233 r_chiral_restr 0.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.175 r_dihedral_angle_3_deg 14.53 r_dihedral_angle_4_deg 11.772 r_dihedral_angle_1_deg 3.87 r_angle_refined_deg 0.854 r_scangle_it 0.663 r_mcangle_it 0.432 r_scbond_it 0.374 r_mcbond_it 0.233 r_chiral_restr 0.051 r_bond_refined_d 0.009 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7393 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction macChess data collection DENZO data reduction SCALEPACK data scaling BALBES phasing