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Full-length dimer of DNA-Damage Response Protein C from Deinococcus radiodurans - Crystal form xMJ7124
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7UDI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.5 ul of protein solution was mixed with 1.5 uL of crystallization solution and hung upside-down in a sealed chamber containing 1mL of well solution
Protein solution:
140uM DdrC,
200mM Sodium sulfate,
1mM Magnesium chloride,
20mM Sodium citrate / Citric acid, pH 6.5
Crystallization solution (Wizard Classics 1 #22)
10% (v/v) 2-propanol
100mM Tris-base/HCl, pH 8.5
Well solution:
1.5M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.48 64.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.039 α = 90 b = 111.039 β = 90 c = 101.493 γ = 120
Symmetry Space Group P 32 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 RIGAKU SATURN 944+ 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541780
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.277 96.163 100 0.179 0.064 0.998 9.9 8.9 5236 170.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.277 4.351 100 0.937 0.344 0.889 2.9 9.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 4.28 69.81 1.34 5208 243 99.45 0.2567 0.2524 0.2504 0.3457 0.3387 215.44
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 11.3862 f_angle_d 0.9776 f_chiral_restr 0.0507 f_plane_restr 0.0079 f_bond_d 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3422 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection autoPROC data processing XDS data reduction pointless data scaling PHASER phasing PHENIX refinement