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Crystal structure of CreD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 293 0.1 M Tris-HCl, pH 8.2-8.5 containing 1.8-2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.81 α = 90 b = 98.22 β = 90 c = 124.51 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 6M 2016-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 2.18 19.918 99.2 0.074 0.084 0.999 13.63 4.416 47180 -3 32.68
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 2.18 2.24 94.6 0.49 0.586 0.903 2.45 3.163
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1RE5 2.18 19.918 1.36 47156 2370 99.32 0.1851 0.1834 0.1869 0.2147 0.2195 Random selection
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 2.605 f_angle_d 0.809 f_chiral_restr 0.043 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3045 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing