☰ Navigation Tabs
Structure of a putative Ubiquitin-conjugating enzyme E2 from Brugia malayi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 28mg/ml BrmaA.00250.a, 200mM sodium malonate dibasic, 20% PEG3350, 20% ethylene glycol for cryoprotection. , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.85 α = 90 b = 52.03 β = 90 c = 108.61 γ = 90
Symmetry Space Group P 21 2 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 MARMOSAIC 300 mm CCD 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.7 50 99.9 0.056 19.48 22536 -3 26.511
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 1.7 1.74 100 0.424 3.92
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 2GRN 1.7 46.97 22499 1152 99.93 0.172 0.1702 0.1811 0.207 0.2157 RANDOM 21.6398
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] 0.53 -0.36 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.063 r_dihedral_angle_4_deg 20.359 r_dihedral_angle_3_deg 13.062 r_dihedral_angle_1_deg 5.722 r_angle_refined_deg 1.338 r_mcangle_it 1.133 r_angle_other_deg 0.756 r_mcbond_it 0.666 r_mcbond_other 0.664 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.063 r_dihedral_angle_4_deg 20.359 r_dihedral_angle_3_deg 13.062 r_dihedral_angle_1_deg 5.722 r_angle_refined_deg 1.338 r_mcangle_it 1.133 r_angle_other_deg 0.756 r_mcbond_it 0.666 r_mcbond_other 0.664 r_chiral_restr 0.079 r_bond_refined_d 0.009 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 1322 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction