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Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Polaromonas sp. JS6 66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.8 M LiCl, 0.1M Tris:HCl, pH 8.5, 32% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.431 α = 96.93 b = 68.158 β = 90.68 c = 77.369 γ = 94.38
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 315 2012-06-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
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 1.7 50 94.6 0.06 8.6 1.9 266267
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 1.7 1.73 77.8 0.783 1.6 10915
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 SAD THROUGHOUT 1.7 19.96 135460 6801 96.04 0.1913 0.1899 0.2176 0.2123 RANDOM 34.3086
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] 0.01 0.11 0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.916 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_4_deg 11.268 r_dihedral_angle_1_deg 6.071 r_angle_refined_deg 1.327 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9758 Nucleic Acid Atoms Solvent Atoms 927 Heterogen Atoms 38
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction PHENIX phasing