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X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ pdb entry 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 CdCl2, PEG MME 2000 (w/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.872 α = 90 b = 50.395 β = 90 c = 92.941 γ = 90
Symmetry Space Group P 21 21 21
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 2004-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97926 APS 17-ID
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 1.3 20 51444 41081
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.4 35
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 pdb entry 1UBQ 1.3 20 38985 2096 79.86 0.19637 0.19522 0.2049 0.21769 0.2264 RANDOM 7.427
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] -0.53 0.39 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.324 r_dihedral_angle_4_deg 20.741 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.497 r_scangle_it 4.047 r_scbond_it 3.235 r_mcangle_it 1.902 r_angle_other_deg 1.806 r_angle_refined_deg 1.706 r_mcbond_it 1.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.324 r_dihedral_angle_4_deg 20.741 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.497 r_scangle_it 4.047 r_scbond_it 3.235 r_mcangle_it 1.902 r_angle_other_deg 1.806 r_angle_refined_deg 1.706 r_mcbond_it 1.652 r_mcbond_other 0.374 r_symmetry_vdw_refined 0.301 r_symmetry_hbond_refined 0.296 r_nbd_refined 0.267 r_xyhbond_nbd_refined 0.261 r_symmetry_vdw_other 0.241 r_nbd_other 0.188 r_chiral_restr 0.17 r_metal_ion_refined 0.138 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1745 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing