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Crystal structure of Dronpa-Cu2+
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 2.33 47.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.268 α = 115.89 b = 105.961 β = 107.68 c = 108.03 γ = 94.12
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 2.84 30 93.6 19.27 2.9 58449
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 2.84 29.94 55512 2936 93.19 0.2157 0.2141 0.2157 0.2451 0.2426 RANDOM 56.616
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] -0.14 -0.1 -2.02 -1.11 0.7 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.123 r_dihedral_angle_3_deg 16.907 r_dihedral_angle_4_deg 12.063 r_dihedral_angle_1_deg 6.377 r_mcangle_it 6.377 r_mcbond_it 4.015 r_mcbond_other 4.014 r_angle_refined_deg 1.713 r_angle_other_deg 1.607 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.123 r_dihedral_angle_3_deg 16.907 r_dihedral_angle_4_deg 12.063 r_dihedral_angle_1_deg 6.377 r_mcangle_it 6.377 r_mcbond_it 4.015 r_mcbond_other 4.014 r_angle_refined_deg 1.713 r_angle_other_deg 1.607 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20315 Nucleic Acid Atoms Solvent Atoms 61 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