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Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 sodium cacodylate
ammonium solfate
magnesium acetate
Crystal Properties Matthews coefficient Solvent content 4.56 73.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.37 α = 90 b = 176.6 β = 105.12 c = 59.9 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 RAYONIX MX-225 2017-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.1 48.376 99.7 0.197 0.229 0.988 7.05 3.801 20596 -3 57.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.29 99.5 0.744 0.867 0.928 1.96 3.819
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 2czw 3.1 48.376 1.36 20436 1021 99.03 0.2261 0.2249 0.2267 0.2472 0.2512 72.6709
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 17.449 f_angle_d 0.465 f_chiral_restr 0.031 f_plane_restr 0.004 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms 2264 Solvent Atoms Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction