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Crystal structure of RSP in complex with beta-NADH
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 6.5 298 0.16M zinc acetate, 0.08M sodium cacodylate, 14.4% PEG 8000, 20% glycerol, 5mM alpha-NADH, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.793 α = 90 b = 75.123 β = 94.37 c = 59.208 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 ADSC QUANTUM 315r 2012-10-16 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 2.05 25 98.1 0.053 26.7 4 31202 30614 3 35.7
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 2.05 2.12 88.5 0.434 2.2 3.4
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 PDB 3WG9 2.05 22.61 29306 1435 100 0.1801 0.17722 0.1898 0.23676 0.2431 RANDOM 53.265
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] 1.69 2.27 -1.58 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.105 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 17.6 r_dihedral_angle_1_deg 6.409 r_scangle_it 5.356 r_scbond_it 3.434 r_mcangle_it 2.311 r_angle_refined_deg 1.714 r_mcbond_it 1.274 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.105 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 17.6 r_dihedral_angle_1_deg 6.409 r_scangle_it 5.356 r_scbond_it 3.434 r_mcangle_it 2.311 r_angle_refined_deg 1.714 r_mcbond_it 1.274 r_chiral_restr 0.122 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 3336 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 104
Software Software Software Name Purpose Blu-Ice data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing REFMAC refinement