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Crystal structure of an engineered metal-free RIDC1 variant containing five disulfide bonds.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Drop consists of 1 uL of 45% MPD, and 0.1 M Bis Tris (pH 6.5) mixed with 1.5 uL of 2.8 mM protein
Crystal Properties Matthews coefficient Solvent content 2.15 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.594 α = 90 b = 77.534 β = 90 c = 88.063 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD 2016-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 38.77 99.8 0.067 14.9 6.9 17325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.4 0.23 5.7 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 4JEA 2.4 38.77 16402 866 99.61 0.22716 0.22501 0.2256 0.26701 0.2663 RANDOM 56.147
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] 0.29 1.32 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.128 r_dihedral_angle_3_deg 16.997 r_dihedral_angle_4_deg 10.03 r_dihedral_angle_1_deg 5.041 r_mcangle_it 3.051 r_mcbond_it 1.809 r_mcbond_other 1.807 r_angle_refined_deg 1.302 r_angle_other_deg 0.983 r_chiral_restr 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.128 r_dihedral_angle_3_deg 16.997 r_dihedral_angle_4_deg 10.03 r_dihedral_angle_1_deg 5.041 r_mcangle_it 3.051 r_mcbond_it 1.809 r_mcbond_other 1.807 r_angle_refined_deg 1.302 r_angle_other_deg 0.983 r_chiral_restr 0.062 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3222 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing