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Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray diffraction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 283.15 48% MPD
20% IPA
25 mM sodium acetate buffer pH 4.7
20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP
Crystal Properties Matthews coefficient Solvent content 1.99 38.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.89 α = 90 b = 36.489 β = 98.67 c = 48.94 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 6M 2017-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9795 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.12 27.571 97.43 0.01784 0.02524 0.01784 0.999 12.98 2 69779 7.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.16
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 MOLECULAR REPLACEMENT FREE R-VALUE 2QMT 1.12 27.571 1.36 69779 3802 95.06 0.1379 0.1369 0.1462 0.1561 0.1623
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 20.938 f_angle_d 1.081 f_chiral_restr 0.086 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 868 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHENIX model building PHASER phasing XDS data scaling