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Crystal structure of RSP in complex with alpha-NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WG9 PDB 3WG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 20% w/v PEG 3350, 0.4M ammonium sulfate, 0.1M Bis-Tris, plus 5mM alpha-NAD+, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.816 α = 90 b = 74.137 β = 90 c = 54.764 γ = 90
Symmetry Space Group P 21 21 2
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 315r 2010-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 2.1 25 99.4 0.072 20.7 5 34128 33930 3 31.3
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 2.1 2.18 96.6 0.456 2.5 4.7
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 PDB 3WG9 2.1 24.9 32146 1596 100 0.18198 0.17934 0.23124 0.2209 RANDOM 44.519
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] -0.52 -1.45 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.597 r_dihedral_angle_3_deg 18.218 r_dihedral_angle_4_deg 17.395 r_dihedral_angle_1_deg 6.954 r_scangle_it 5.613 r_scbond_it 3.633 r_mcangle_it 2.447 r_angle_refined_deg 1.818 r_mcbond_it 1.4 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.597 r_dihedral_angle_3_deg 18.218 r_dihedral_angle_4_deg 17.395 r_dihedral_angle_1_deg 6.954 r_scangle_it 5.613 r_scbond_it 3.633 r_mcangle_it 2.447 r_angle_refined_deg 1.818 r_mcbond_it 1.4 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3430 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 118
Software Software Software Name Purpose Blu-Ice data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing REFMAC refinement