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Crystal Structure of UbcH8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C4Z PDB ENTRY 1C4Z CHAIN D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.4 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.231 α = 90 b = 35.486 β = 104.55 c = 92.58 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 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 0.900 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 2.1 100 97.7 0.046 16.8 3.65 19900 -3 36.2
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) 2.1 2.18 94.9 0.237
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 (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 PDB ENTRY 1C4Z CHAIN D 2.1 20 18854 1011 97.76 0.20952 0.20952 0.20658 0.2051 0.26726 0.2652 RANDOM 37.989
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] -1.48 0.28 2.03 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.674 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_4_deg 10.96 r_dihedral_angle_1_deg 5.124 r_scangle_it 3.595 r_scbond_it 2.194 r_mcangle_it 1.396 r_angle_refined_deg 1.325 r_mcbond_it 0.932 r_symmetry_vdw_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.674 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_4_deg 10.96 r_dihedral_angle_1_deg 5.124 r_scangle_it 3.595 r_scbond_it 2.194 r_mcangle_it 1.396 r_angle_refined_deg 1.325 r_mcbond_it 0.932 r_symmetry_vdw_refined 0.337 r_nbtor_refined 0.31 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2454 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing