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Crystal structure of Dynamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AKA PDB ENTRY 2AKA CHAIN B, PDB ENTRY 2DYN CHAIN B, PDB ENTRY 3LJB CHAIN B experimental model PDB 2DYN PDB ENTRY 2AKA CHAIN B, PDB ENTRY 2DYN CHAIN B, PDB ENTRY 3LJB CHAIN B experimental model PDB 3LJB PDB ENTRY 2AKA CHAIN B, PDB ENTRY 2DYN CHAIN B, PDB ENTRY 3LJB CHAIN B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.7 52.5 MM TRIS.HCL PH 7.7, 175 MM NACL, 32.5 MM NANO3, 20 % V/V PEG 400, 0.97 MM BETA-MERCAPTOETHANOL, 31.9 MICROM DYN1 G397D DELTA PRD
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.45 α = 90 b = 191.61 β = 90 c = 60.52 γ = 90
Symmetry Space Group C 2 2 21
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 2011-04-17 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) 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 3.1 95.8 96.7 0.07 15.4 4.1 18735 -3 101.701
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 3.1 3.18 66.2 0.88 1.9 4.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2AKA CHAIN B, PDB ENTRY 2DYN CHAIN B, PDB ENTRY 3LJB CHAIN B 3.1 95.805 1.34 18731 956 96.73 0.2153 0.2123 0.272 0.2688 114.41
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] 9.0208 2.8708 -11.8916
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.046 f_angle_d 1.098 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5407 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing