☰ Navigation Tabs
Crystal Structure of Monoclinic Rabbit Muscle Lactate Dehydrogenase with Four Tetramers as the Asymmetric Unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LDH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Sitting drop composed of equal amounts of 20% PEG 3350 in .10 M Tris buffer pH 7.0 and a 30 mg/ml stock protein solution containing 0.1 M Tris pH 7.0. Reservoir 20% PEG 3350 in water.
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.572 α = 90 b = 100.838 β = 101.23 c = 223.102 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 298 AREA DETECTOR SDMS bent crystal monochromator 1995-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.4 60 88 0.13 0.12 0.97 7.4 6.5 3 52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.45 22 0.28 0.28 0.54 3.3 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) 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 MOLECULAR REPLACEMENT THROUGHOUT 6LDH 2.42 60 123133 13675 51.51 0.18412 0.18092 0.1862 0.21338 0.2158 RANDOM 52.132
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] -1.27 1.69 2.47 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 24.182 r_dihedral_angle_3_deg 15.106 r_long_range_B_refined 9.963 r_long_range_B_other 9.963 r_scangle_other 6.459 r_dihedral_angle_1_deg 5.174 r_mcangle_it 4.954 r_mcangle_other 4.954 r_scbond_it 3.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 24.182 r_dihedral_angle_3_deg 15.106 r_long_range_B_refined 9.963 r_long_range_B_other 9.963 r_scangle_other 6.459 r_dihedral_angle_1_deg 5.174 r_mcangle_it 4.954 r_mcangle_other 4.954 r_scbond_it 3.908 r_scbond_other 3.908 r_mcbond_it 3.041 r_mcbond_other 3.04 r_angle_refined_deg 1.281 r_angle_other_deg 0.67 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 40944 Nucleic Acid Atoms Solvent Atoms 1380 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing