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Crystal structure of the FYVE domain of endofin (ZFYVE16) at 1.1A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 20% PEG 3350, 0.2 M NaNO3, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 1.73 28.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.944 α = 90 b = 42.944 β = 90 c = 76.879 γ = 90
Symmetry Space Group P 43 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 2011-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9611 Diamond I04
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 1.09 28.64 99.9 0.082 10.8 5.2 30800 30734 6.6
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 1.09 1.15 99.9 0.748 2 4.6 4404
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.09 22.01 2 30734 29183 1550 99.78 0.168 0.14244 0.14182 0.1497 0.15423 0.1567 RANDOM 13.388
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] 0.2 0.2 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.763 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 12.062 r_dihedral_angle_1_deg 6.421 r_sphericity_bonded 2.375 r_angle_refined_deg 1.676 r_angle_other_deg 1.014 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.763 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 12.062 r_dihedral_angle_1_deg 6.421 r_sphericity_bonded 2.375 r_angle_refined_deg 1.676 r_angle_other_deg 1.014 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 581 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 6
Software Software Software Name Purpose GDA data collection SHARP phasing REFMAC refinement XDS data reduction SCALA data scaling