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Crystal structure of KRED F147L/L153Q/Y190P variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.61 α = 90 b = 55.44 β = 103.94 c = 128.95 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 PIXEL DECTRIS PILATUS 6M 2020-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97913 SSRF BL17U1
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 1.855 61.93 98.8 0.069 0.075 0.03 0.998 15.4 6.2 73460 24.5825724457
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.855 1.9 93.4 0.504 0.574 0.265 0.822 2.7 4.4
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 4RF2 1.855715608 31.9017853489 1.34351255351 73442 2000 98.7468739075 0.159038385072 0.157938085445 0.1621 0.198109482186 0.1694 26.0898997739
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 7.29436490524 f_angle_d 0.950603032299 f_chiral_restr 0.0579075180397 f_bond_d 0.0062425572379 f_plane_restr 0.00471698383386
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7399 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 197
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing