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Human B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IOZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 4000, Ammonium acetate, Na citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.18 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.397 α = 90 b = 160.443 β = 90 c = 59.366 γ = 90
Symmetry Space Group P 21 21 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 MACSCIENCE 2001-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.5418
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 3 30 0.166 6.4 2.7 27214 24742 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) 3 3.16 79.1 0.302 2.6
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1IOZ 3 29.88 24474 23299 1242 90.52 0.2206 0.21527 0.32053 0.2945 RANDOM 52.254
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] -2.42 2.71 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.001 r_scangle_it 2.668 r_angle_refined_deg 2.017 r_scbond_it 1.554 r_angle_other_deg 1.381 r_mcangle_it 1.161 r_mcbond_it 0.633 r_symmetry_vdw_other 0.332 r_symmetry_vdw_refined 0.311 r_symmetry_hbond_refined 0.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.001 r_scangle_it 2.668 r_angle_refined_deg 2.017 r_scbond_it 1.554 r_angle_other_deg 1.381 r_mcangle_it 1.161 r_mcbond_it 0.633 r_symmetry_vdw_other 0.332 r_symmetry_vdw_refined 0.311 r_symmetry_hbond_refined 0.275 r_nbd_refined 0.266 r_xyhbond_nbd_refined 0.258 r_nbd_other 0.254 r_xyhbond_nbd_other 0.202 r_chiral_restr 0.118 r_nbtor_other 0.092 r_symmetry_hbond_other 0.084 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10220 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing