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Crystal structure of the aminopeptidase N family protein Q5QTY1 from Idiomarina loihiensis. Northeast Structural Genomics Consortium Target IlR60.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch crystallization under oil 6.8 277 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 45% PEG/Tacsimate pH 6.8 (Hampton research HR2-092), 45% Silver Bullet (Hampton research HR2-096, G11), 0.1 M sodium citrate., Microbatch crystallization under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.32 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.657 α = 90 b = 119.657 β = 90 c = 220.134 γ = 120
Symmetry Space Group P 62 2 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 MARMOSAIC 325 mm CCD 2012-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97900 SSRL BL9-2
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 2.394 50 100 0.115 27.3 11.7 49.99
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 2.4 2.49 100 0.978 2.05 11.7 27765
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.394 42.325 1.38 69442 3489 99.96 0.191 0.19 0.19 0.209 0.2074 RANDOM 51.705
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] 2.12 2.12 -4.239
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.504 f_angle_d 1.387 f_chiral_restr 0.104 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4709 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling SHELXDE phasing