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Rpn11 homolog from Caldiarchaeum Subterraneum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 100 mM HEPES pH 7.0, 15% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.452 α = 90 b = 65.614 β = 90 c = 99.708 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M-F 2015-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.65 33.8 99.7 0.055 0.999 18.8 6.86 51685
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.75 98.2 0.973 0.791 1.77 6.29
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 4OCL 1.65 33.8 49099 2585 99.74 0.16698 0.16576 0.1782 0.19025 0.2047 RANDOM 33.662
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] 0.83 -1.28 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.791 r_dihedral_angle_4_deg 22.382 r_dihedral_angle_3_deg 12.671 r_long_range_B_refined 7.852 r_long_range_B_other 7.754 r_dihedral_angle_1_deg 6.049 r_scangle_other 4.549 r_mcangle_it 3.035 r_mcangle_other 3.035 r_scbond_it 2.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.791 r_dihedral_angle_4_deg 22.382 r_dihedral_angle_3_deg 12.671 r_long_range_B_refined 7.852 r_long_range_B_other 7.754 r_dihedral_angle_1_deg 6.049 r_scangle_other 4.549 r_mcangle_it 3.035 r_mcangle_other 3.035 r_scbond_it 2.986 r_scbond_other 2.972 r_mcbond_it 2.075 r_mcbond_other 2.063 r_angle_refined_deg 1.89 r_angle_other_deg 1.316 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.007 r_gen_planes_other 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2713 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing