☰ Navigation Tabs
Plasmodium falciparum lactate dehydrogenase complexed with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.3 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.136 α = 90 b = 87.124 β = 90 c = 92.212 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 CCD ADSC QUANTUM 4 2001-01-01 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 2 30 98.3 0.044 28.5 4 21912 21521 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 2 2.09 99.8 0.105 10.1 2693
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LDG 2.01 29.75 21192 20101 1091 95.86 0.14521 0.14521 0.14311 0.1496 0.18354 RANDOM 9.879
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] -0.9 1 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.821 r_scangle_it 4.273 r_scbond_it 2.819 r_angle_refined_deg 1.815 r_mcangle_it 1.665 r_angle_other_deg 1.646 r_mcbond_it 0.985 r_symmetry_hbond_refined 0.468 r_symmetry_vdw_other 0.355 r_symmetry_vdw_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.821 r_scangle_it 4.273 r_scbond_it 2.819 r_angle_refined_deg 1.815 r_mcangle_it 1.665 r_angle_other_deg 1.646 r_mcbond_it 0.985 r_symmetry_hbond_refined 0.468 r_symmetry_vdw_other 0.355 r_symmetry_vdw_refined 0.293 r_nbd_other 0.233 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.102 r_nbtor_other 0.083 r_gen_planes_other 0.039 r_gen_planes_refined 0.027 r_bond_refined_d 0.024 r_bond_other_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2383 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing