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Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 28% (w/v) PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.37 α = 90 b = 47.601 β = 90 c = 82.34 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 Bruker DIP-6040 2004-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 1.6 41.204 100 0.054 16.8 6.9 22178 -3
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) 1.6 1.66 99.9 0.331
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 2Z6P 1.6 41.2 20992 1133 99.99 0.1956 0.19429 0.1934 0.22125 0.2185 RANDOM 18.727
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] 0.17 0.32 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.528 r_dihedral_angle_4_deg 14.221 r_dihedral_angle_3_deg 12.082 r_dihedral_angle_1_deg 5.251 r_scangle_it 3.445 r_scbond_it 2.088 r_mcangle_it 1.209 r_angle_refined_deg 1.145 r_mcbond_it 0.739 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.528 r_dihedral_angle_4_deg 14.221 r_dihedral_angle_3_deg 12.082 r_dihedral_angle_1_deg 5.251 r_scangle_it 3.445 r_scbond_it 2.088 r_mcangle_it 1.209 r_angle_refined_deg 1.145 r_mcbond_it 0.739 r_nbtor_refined 0.31 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1364 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing