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Crystal structure of NADP-dependent dehydrogenase from Rhodobacter sphaeroides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZQB
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 # 72 (20%w/v PEG 3350, 0.2M Li nitrate) 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
Crystal Properties Matthews coefficient Solvent content 2 38.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.048 α = 90 b = 80.085 β = 93.69 c = 61.33 γ = 90
Symmetry Space Group C 1 2 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 300 mm CCD 2014-11-06 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 2.2 50 96.4 0.074 0.074 0.085 0.04 8.7 4.4 26059 -3 41.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 79.5 0.527 0.602 0.286 0.893 2.2 3.9 1079
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 4ZQB 2.2 50 26059 1253 96.36 0.1973 0.1945 0.1976 0.252 0.2476 RANDOM 62.532
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] -1.11 1.16 7.09 -6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_4_deg 22.018 r_dihedral_angle_3_deg 13.702 r_dihedral_angle_1_deg 5.807 r_mcangle_it 2.457 r_angle_refined_deg 1.657 r_mcbond_other 1.58 r_mcbond_it 1.579 r_angle_other_deg 1.271 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_4_deg 22.018 r_dihedral_angle_3_deg 13.702 r_dihedral_angle_1_deg 5.807 r_mcangle_it 2.457 r_angle_refined_deg 1.657 r_mcbond_other 1.58 r_mcbond_it 1.579 r_angle_other_deg 1.271 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4537 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 data reduction HKL-3000 phasing HKL-3000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction