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Plasmodium vivax ubiquitin conjugating enzyme E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 22% PEG3350, 0.19M Ca(AC)2, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 1.98 37.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.004 α = 90 b = 58.004 β = 90 c = 117.114 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV VeriMax HR 2006-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.86 30 99.9 0.064 0.064 10.1 14.4 10446 10446 31.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.86 1.89 99.8 0.978 0.978 2.38 13.8 495
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 1Z2U 1.86 30 10446 9639 780 99.91 0.20863 0.20863 0.20438 0.2071 0.26251 0.2073 RANDOM 31.603
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] 0.63 0.32 0.63 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_dihedral_angle_3_deg 12.407 r_dihedral_angle_4_deg 8.091 r_dihedral_angle_1_deg 4.633 r_scangle_it 3.831 r_mcangle_it 3.546 r_scbond_it 2.813 r_mcbond_it 2.551 r_angle_refined_deg 1.454 r_symmetry_vdw_refined 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.592 r_dihedral_angle_3_deg 12.407 r_dihedral_angle_4_deg 8.091 r_dihedral_angle_1_deg 4.633 r_scangle_it 3.831 r_mcangle_it 3.546 r_scbond_it 2.813 r_mcbond_it 2.551 r_angle_refined_deg 1.454 r_symmetry_vdw_refined 0.355 r_nbtor_refined 0.307 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.077 r_bond_refined_d 0.017 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 882 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data scaling PHASER phasing Coot model building SOLVE phasing RESOLVE phasing ARP/wARP model building