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Ubiquitin fold modifier conjugating enzyme from Leishmania major (probable)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 293 protein buffer 25 mM HEPES pH 7.5, 120 mM NaCl; crystallization buffer 100 mM Na Cacodylate, 300 mM Ammonium Sulfate,, 30% PEG 4000, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.274 α = 90 b = 34.133 β = 99.32 c = 126.774 γ = 90
Symmetry Space Group P 1 21 1
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 315 2003-08-12 MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9784 ALS 8.2.2
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 2.2 50 91.4 0.102 11.4 23133 23133 30.2
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 2.2 2.37 70.1 0.394 2.2 1776
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 2in1 2.2 50 23096 1187 91.53 0.217 0.214 0.2235 0.273 0.2721 RANDOM 12.42
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] 1.79 0.54 -0.45 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.802 r_dihedral_angle_4_deg 21.469 r_dihedral_angle_3_deg 15.091 r_dihedral_angle_1_deg 5.359 r_scangle_it 2.124 r_scbond_it 1.347 r_angle_refined_deg 1.22 r_angle_other_deg 0.826 r_mcangle_it 0.804 r_mcbond_it 0.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.802 r_dihedral_angle_4_deg 21.469 r_dihedral_angle_3_deg 15.091 r_dihedral_angle_1_deg 5.359 r_scangle_it 2.124 r_scbond_it 1.347 r_angle_refined_deg 1.22 r_angle_other_deg 0.826 r_mcangle_it 0.804 r_mcbond_it 0.425 r_mcbond_other 0.089 r_chiral_restr 0.071 r_bond_refined_d 0.01 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 3828 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling BALBES phasing