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Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KBQ N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1) experimental model PDB 1QAV N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1) experimental model PDB 1KW4 N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1) experimental model PDB 1PK1 N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.2M CaAc2, 0.1M HEPES, pH 7.5, 18% (w/v) polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.603 α = 90 b = 57.775 β = 104.63 c = 59.505 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 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2009-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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 2.3 30.8 93 0.086 10.9 16268 2 2 24.1
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) 2.3 2.42 93 0.086 0.21 10.9 4 16268
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 N-domain (PDB id:2KBQ), PDZ domain (PDB ID:1QAV), SAM domain (PDB ID 1KW4 and 1PK1) 2.3 28.89 3.3 16268 15430 825 92.53 0.21262 0.21037 0.2092 0.25568 0.2573 RANDOM 25.719
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] 1.56 0.18 -0.81 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.187 r_dihedral_angle_4_deg 16.891 r_dihedral_angle_3_deg 14.667 r_dihedral_angle_1_deg 4.434 r_angle_refined_deg 0.955 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2139 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALEPACK data scaling