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X-ray Crystal Structure of a Chemically Synthesized Ubiquitin
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 293.0K
Crystal Properties Matthews coefficient Solvent content 2.1 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.776 α = 90 b = 50.476 β = 90 c = 92.649 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 MARRESEARCH 2004-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.97926 APS 5ID-B
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 1.39 20 64.69 42005 27173
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 1.39 1.55 19.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.39 20 42005 25796 1377 64.69 0.1728 0.17282 0.171 0.1762 0.20702 0.2133 RANDOM 10.358
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] -0.71 -0.53 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_4_deg 21.743 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 5.618 r_scangle_it 4.336 r_scbond_it 3.422 r_mcangle_it 1.865 r_angle_other_deg 1.703 r_mcbond_it 1.669 r_angle_refined_deg 1.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.673 r_dihedral_angle_4_deg 21.743 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 5.618 r_scangle_it 4.336 r_scbond_it 3.422 r_mcangle_it 1.865 r_angle_other_deg 1.703 r_mcbond_it 1.669 r_angle_refined_deg 1.608 r_symmetry_vdw_refined 0.374 r_nbd_refined 0.264 r_metal_ion_refined 0.258 r_symmetry_vdw_other 0.254 r_xyhbond_nbd_refined 0.219 r_symmetry_hbond_refined 0.214 r_nbd_other 0.2 r_chiral_restr 0.089 r_nbtor_other 0.088 r_mcbond_other 0.042 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1719 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling CNS phasing