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Crystal structure of human ubiquitin-conjugating enzyme UbcH5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QCQ PDB ENTRY 1QCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.621 α = 90 b = 50.565 β = 90 c = 66.043 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 CCD MIRRORS 2004-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 2.35 30.15 96.8 0.06 12.5 2.4 89448 2 40.6
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 2.35 2.47 87.7 0.51 2 2.2
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 PDB ENTRY 1QCQ 2.35 30.14 11589 878 96.8 0.232 0.232 0.2371 0.272 0.2681 RANDOM 48.06
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] -5.05 1.29 3.76
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.07 c_mcangle_it 2.01 c_angle_deg 1.371 c_scbond_it 1.3 c_mcbond_it 1.14 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.07 c_mcangle_it 2.01 c_angle_deg 1.371 c_scbond_it 1.3 c_mcbond_it 1.14 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2343 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling PHASER phasing