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Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PP8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.2 ul of 10.5 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition # 23 (0.1M Bis-Tris, 25%w/v PEG 3350, 0.2M Li sulfate pH=6.5 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin and 10 mM NADP solution at 289 K for 3 hours.
Crystal Properties Matthews coefficient Solvent content 2.63 53.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.489 α = 90 b = 71.489 β = 90 c = 244.364 γ = 120
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 300 mm CCD Beryllium Lenses 2014-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.85 50 99.3 0.161 0.161 0.171 0.073 4.7 6.2 60347 59896 -3 23.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 97.1 0.428 0.649 2 6.2 2955
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3PP8 1.85 50 59625 2948 99.41 0.1665 0.1649 0.1997 0.192 RANDOM 27.931
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] -0.35 -0.18 -0.35 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.836 r_dihedral_angle_4_deg 19.48 r_dihedral_angle_3_deg 12.205 r_dihedral_angle_1_deg 5.439 r_angle_refined_deg 1.565 r_angle_other_deg 1.263 r_mcangle_it 0.938 r_mcbond_other 0.585 r_mcbond_it 0.584 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.836 r_dihedral_angle_4_deg 19.48 r_dihedral_angle_3_deg 12.205 r_dihedral_angle_1_deg 5.439 r_angle_refined_deg 1.565 r_angle_other_deg 1.263 r_mcangle_it 0.938 r_mcbond_other 0.585 r_mcbond_it 0.584 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4762 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 139
Software Software Software Name Purpose PDB_EXTRACT data extraction Coot model building REFMAC refinement HKL-3000 phasing MOLREP phasing HKL-3000 data scaling HKL-3000 data reduction BLU-MAX data collection