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Crystal Structure of the 35-36 MoaD Insertion Mutant of Ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GBM PDB ENTRY 2GBM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.9 293.15 24-30% PEG 4000, 50-80 mM Cadmium Chloride, 100 mM Sodium Acetate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.05 39.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.465 α = 90 b = 54.807 β = 90 c = 92.627 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 4 2005-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00808 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 5 99.4 0.135 5.9 3.86 14781 14696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 100 100 0.421 2.5 3.9 1447
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2GBM 2 4.99 14781 14668 745 99.26 0.21938 0.21938 0.21583 0.2284 0.28971 0.3013 RANDOM 22.689
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] -0.02 0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.294 r_dihedral_angle_3_deg 15.577 r_dihedral_angle_4_deg 15.311 r_dihedral_angle_1_deg 5.667 r_scangle_it 2.746 r_scbond_it 1.775 r_angle_refined_deg 1.237 r_mcangle_it 0.965 r_mcbond_it 0.838 r_angle_other_deg 0.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.294 r_dihedral_angle_3_deg 15.577 r_dihedral_angle_4_deg 15.311 r_dihedral_angle_1_deg 5.667 r_scangle_it 2.746 r_scbond_it 1.775 r_angle_refined_deg 1.237 r_mcangle_it 0.965 r_mcbond_it 0.838 r_angle_other_deg 0.795 r_symmetry_metal_ion_refined 0.493 r_symmetry_vdw_refined 0.442 r_xyhbond_nbd_refined 0.256 r_metal_ion_refined 0.243 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.213 r_symmetry_vdw_other 0.202 r_nbd_other 0.179 r_nbtor_refined 0.168 r_mcbond_other 0.142 r_nbtor_other 0.083 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1840 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 13
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection