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HUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 protein solution: 28 mg/ml protein, 100 mM Na-HEPES pH 7.5, 2.5 mM NADH, 1 mM Na Oxamate. Well solution: 12% PEG 8K, 100 mM Na HEPES pH 7.5, 100 mM Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.942 α = 90 b = 158.542 β = 90 c = 266.226 γ = 90
Symmetry Space Group P 21 21 21
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 1999-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX7.2 SRS PX7.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 30 92.3 0.081 14.18 3.51 121781 112344 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.4 89 0.195 5.36 3.53 13397
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 9ldt 2.3 20 105591 5577 90.5 0.20024 0.19722 0.1971 0.25713 0.2547 RANDOM 27.066
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] -0.19 1.02 -0.83
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.949 p_scbond_it 2.516 p_angle_deg 1.815 p_mcangle_it 1.544 p_mcbond_it 0.843 p_xyhbond_nbd 0.172 p_chiral_restr 0.119 p_bond_d 0.017 p_plane_restr 0.006 p_angle_d
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 3.949 p_scbond_it 2.516 p_angle_deg 1.815 p_mcangle_it 1.544 p_mcbond_it 0.843 p_xyhbond_nbd 0.172 p_chiral_restr 0.119 p_bond_d 0.017 p_plane_restr 0.006 p_angle_d p_planar_d p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20497 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 432
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement