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Crystal structure of the PDHK2-L2 complex.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 293 0.1 M sodium acetate (pH 5.3) and 0.5 M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.38 α = 90 b = 120.679 β = 96.03 c = 71.466 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 100 CCD MARMOSAIC 225 mm CCD 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.97625 APS 22-BM
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 71.07 94.9 0.055 18.8 50377
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) 1 2.3 2.3 73.3 0.269 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.3 50 50377 2551 94.94 0.21 0.2078 0.2506 0.2646 RANDOM 53.273
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] -0.12 0.11 0.72 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.318 r_dihedral_angle_3_deg 15.46 r_dihedral_angle_4_deg 14.244 r_dihedral_angle_1_deg 5.081 r_scangle_it 1.522 r_angle_refined_deg 1.009 r_scbond_it 0.933 r_mcangle_it 0.554 r_nbtor_refined 0.301 r_mcbond_it 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.318 r_dihedral_angle_3_deg 15.46 r_dihedral_angle_4_deg 14.244 r_dihedral_angle_1_deg 5.081 r_scangle_it 1.522 r_angle_refined_deg 1.009 r_scbond_it 0.933 r_mcangle_it 0.554 r_nbtor_refined 0.301 r_mcbond_it 0.285 r_metal_ion_refined 0.232 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.135 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7221 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling COMO phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction