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Re-refinement of Crystal Structure of NosGet3d, the All4481 protein from Nostoc sp. PCC 7120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IGF re-refinement of 3IGF using the data from 3IGF. PDB entry 3IGF was solved by SAD-phasing.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.15 291 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 100mM MES (pH 6.15), 18% PEG3350, and 100mM potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.17 α = 90 b = 55.553 β = 98.87 c = 122.363 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 4 2009-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97908 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.98 27.52 89.2 0.06 0.06 18.8 3.3 110202 28.11
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) 1 2 2.07 0.288 0.28 3.1
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 3IGF 1.98 27.52 1 54162 2621 94.34 0.1905 0.1889 0.1887 0.2209 0.2203 42.26
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 5.4395 f_angle_d 0.758 f_chiral_restr 0.0493 f_plane_restr 0.0147 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5528 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement REFMAC refinement CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling SnB phasing Coot model building