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Plasmodium falciparum lactate dehydrogenase complexed with 2-({4-chloro-[hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LDG PDB ENTRY 1LDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.41 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.568 α = 90 b = 85.393 β = 90 c = 92.263 γ = 90
Symmetry Space Group I 2 2 2
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 MARRESEARCH 2001-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 1.7 30 95.3 0.058 23.2 4.5 35317 33657 2 2
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 1.7 1.78 92.2 0.207 5.3 4 4018
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LDG 1.7 29.36 33009 31329 1680 93.46 0.14561 0.14561 0.14387 0.17884 0.2019 RANDOM 13.233
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] -0.17 0.59 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.522 r_scangle_it 3.877 r_scbond_it 2.382 r_angle_refined_deg 1.435 r_mcangle_it 1.357 r_angle_other_deg 1.242 r_mcbond_it 0.752 r_nbd_refined 0.33 r_symmetry_vdw_other 0.301 r_nbd_other 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.522 r_scangle_it 3.877 r_scbond_it 2.382 r_angle_refined_deg 1.435 r_mcangle_it 1.357 r_angle_other_deg 1.242 r_mcbond_it 0.752 r_nbd_refined 0.33 r_symmetry_vdw_other 0.301 r_nbd_other 0.238 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.143 r_nbtor_other 0.086 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing