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Crystal Structure of Yeast UBP3-associated Protein BRE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 300 PEG 3350, Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.909 α = 90 b = 90.909 β = 90 c = 194.896 γ = 120
Symmetry Space Group P 61 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 CCD ADSC QUANTUM 4 2004-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795, 0.9794, 0.9500, 0.9790 NSLS X25
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 50 99.2 0.076 28.3 10.4 28566
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 2.1 2.18 99.6 0.379 8.7 10.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.1 79.06 27084 1445 99.25 0.1896 0.18833 0.1979 0.21299 0.1936 RANDOM 28.153
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] -0.7 -0.35 -0.7 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.81 r_scangle_it 6.637 r_scbond_it 4.089 r_mcangle_it 3.046 r_angle_refined_deg 2.396 r_angle_other_deg 1.642 r_mcbond_it 1.624 r_symmetry_vdw_refined 0.633 r_symmetry_vdw_other 0.421 r_nbd_other 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.81 r_scangle_it 6.637 r_scbond_it 4.089 r_mcangle_it 3.046 r_angle_refined_deg 2.396 r_angle_other_deg 1.642 r_mcbond_it 1.624 r_symmetry_vdw_refined 0.633 r_symmetry_vdw_other 0.421 r_nbd_other 0.274 r_nbd_refined 0.244 r_chiral_restr 0.226 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.192 r_nbtor_other 0.104 r_bond_refined_d 0.032 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.005 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2101 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing