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X-ray structure of the de-novo design amidase at the resolution 1.8A, Northeast Structural Genomics Consortium (NESG) Target OR398
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 100mM HEPES, 42% PEG 200, microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.99 38.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.485 α = 71.07 b = 44.335 β = 75.97 c = 57.515 γ = 86.86
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 315 2013-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
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 1.8 33.5 96.5 0.049 12.5 2.9 78543 27069 -3 27.42
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VIA 1.819 33.445 0.99 27069 2669 94.49 0.205 0.203 0.1986 0.242 0.2363 random 38.123
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.742 f_angle_d 0.953 f_chiral_restr 0.068 f_bond_d 0.007 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2554 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALA data scaling BALBES phasing