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Crystal structure of the computationally designed NNOS-Syntrophin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QAV PDB ENTRY 1QAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 293 0.1M MES, 0.2M LICL, 21.5% PEG 6000. SYNTROPHIN AT 3.6 MG/ML FINAL. NNOS AT 2.6 MG/ML FINAL. 1:1 MIX OF PROTEIN SOLUTION TO PRECIPITANT, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.196 α = 90 b = 102.503 β = 118.61 c = 64.1 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 77.2 CCD ADSC QUANTUM 315 MIRROR1: PLANE PARABOLA PT AND RH-COATED INVAR STEEL, MIRROR2: TOROID (2:1 DEMAGNIFICATION) PT AND RH- COATED SI 2007-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.29 48 100 0.068 0.068 30.532 9.1 31327 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.37 99.8 0.171 0.171 12.043 6
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 ENTRY 1QAV 2.29 47.57 28781 1510 96.6 0.226 0.223 0.2244 0.273 0.2725 RANDOM 15.81
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] 1.31 1.47 -0.26 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.075 r_dihedral_angle_4_deg 13.53 r_dihedral_angle_3_deg 11.167 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.187 r_angle_refined_deg 0.979 r_scbond_it 0.792 r_angle_other_deg 0.765 r_mcangle_it 0.582 r_mcbond_it 0.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.075 r_dihedral_angle_4_deg 13.53 r_dihedral_angle_3_deg 11.167 r_dihedral_angle_1_deg 5.62 r_scangle_it 1.187 r_angle_refined_deg 0.979 r_scbond_it 0.792 r_angle_other_deg 0.765 r_mcangle_it 0.582 r_mcbond_it 0.561 r_symmetry_vdw_other 0.207 r_nbd_other 0.185 r_nbd_refined 0.173 r_nbtor_refined 0.16 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.111 r_symmetry_hbond_refined 0.101 r_nbtor_other 0.077 r_chiral_restr 0.054 r_mcbond_other 0.048 r_xyhbond_nbd_other 0.008 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4702 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling