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Crystal structure of Dronpa-Ni2+
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 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.372 α = 71.11 b = 109.403 β = 85.97 c = 72.087 γ = 61.3
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 1.89 30 94.9 22.185 3 198444
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 1.89 29.03 188475 9967 93.96 0.1534 0.1509 0.161 0.1993 0.2057 RANDOM 24.27
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] -0.75 0.11 -0.04 -0.49 -0.19 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.051 r_dihedral_angle_3_deg 14.707 r_dihedral_angle_4_deg 14.526 r_dihedral_angle_1_deg 7.167 r_mcangle_it 2.799 r_angle_refined_deg 2.064 r_mcbond_it 2.038 r_mcbond_other 2.035 r_angle_other_deg 0.893 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.051 r_dihedral_angle_3_deg 14.707 r_dihedral_angle_4_deg 14.526 r_dihedral_angle_1_deg 7.167 r_mcangle_it 2.799 r_angle_refined_deg 2.064 r_mcbond_it 2.038 r_mcbond_other 2.035 r_angle_other_deg 0.893 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20706 Nucleic Acid Atoms Solvent Atoms 2004 Heterogen Atoms 25
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