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Crystal structure of Dronpa-Co2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295.5 PEG 4000, Tris-HCl, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.32 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.33 α = 115.79 b = 105.479 β = 109.51 c = 109.776 γ = 93.95
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 ADSC QUANTUM 210 2013-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.0 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.17 30 95.1 25.02 3.1 130970
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 2GX2 2.17 29.57 124396 6546 93.13 0.1689 0.1659 0.1771 0.2254 0.2319 RANDOM 31.303
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] 1.96 -0.37 -2.1 0.07 -0.6 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.434 r_dihedral_angle_3_deg 16.2 r_dihedral_angle_4_deg 13.657 r_dihedral_angle_1_deg 7.665 r_mcangle_it 3.487 r_mcbond_it 2.415 r_mcbond_other 2.414 r_angle_refined_deg 1.952 r_angle_other_deg 0.857 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.434 r_dihedral_angle_3_deg 16.2 r_dihedral_angle_4_deg 13.657 r_dihedral_angle_1_deg 7.665 r_mcangle_it 3.487 r_mcbond_it 2.415 r_mcbond_other 2.414 r_angle_refined_deg 1.952 r_angle_other_deg 0.857 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20748 Nucleic Acid Atoms Solvent Atoms 1346 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction