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Plasmodium falciparum TIM complexed to 2-phosphoglycerate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 PEG 1450, Sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.88 34.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.491 α = 90 b = 50.9 β = 91.9 c = 89.01 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 100 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9083 EMBL/DESY, HAMBURG X11
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 1.1 30
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 AB INITIO FREE R 1YDV 1.1 30 170250 2026 87.9 0.1328 0.1328 0.1313 0.1706 0.1294 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 48 4583.45
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.101 s_non_zero_chiral_vol 0.091 s_zero_chiral_vol 0.072 s_similar_adp_cmpnt 0.053 s_anti_bump_dis_restr 0.037 s_angle_d 0.034 s_from_restr_planes 0.0301 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4089 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 33
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing