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Crystal structure of yeast Rpn14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ACP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1M NaCitrate pH4.5, 0.2M MgCl2, 10%(w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 36.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.491 α = 90 b = 141.443 β = 95.67 c = 50.491 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 RAYONIX MX225HE 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 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 1.6 50 97.2 0.048 19.5 3.9 90359 -3
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 1.6 1.62 97.2 0.528 3.7
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 3ACP 1.6 24.47 85676 4505 96.94 0.158 0.15394 0.1521 0.23451 0.2335 RANDOM 28.67
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] -0.03 0.03 0.19 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.483 r_dihedral_angle_4_deg 20.783 r_scangle_it 19.342 r_scbond_it 17.802 r_dihedral_angle_3_deg 17.417 r_rigid_bond_restr 14.997 r_mcangle_it 13.577 r_mcbond_it 12.825 r_dihedral_angle_1_deg 9.05 r_angle_refined_deg 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.483 r_dihedral_angle_4_deg 20.783 r_scangle_it 19.342 r_scbond_it 17.802 r_dihedral_angle_3_deg 17.417 r_rigid_bond_restr 14.997 r_mcangle_it 13.577 r_mcbond_it 12.825 r_dihedral_angle_1_deg 9.05 r_angle_refined_deg 0.94 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6510 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling