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The retroviral-like protease (RVP) domain of human DDI1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ILA pdb entry 2ILA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 21% PEG3350, 0.2 M AMMONIUM PHOSPHATE, 0.1 M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.15 42.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.981 α = 90 b = 41.04 β = 107.62 c = 88.975 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC MIRRORS 2011-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.7 30 97.8 0.043 52.372 6.9 30254 30254 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 73.4 0.314 7.74 5.3 1112
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 MR THROUGHOUT pdb entry 2ILA 1.7 28.27 28725 1499 97.65 0.17686 0.17573 0.1726 0.19871 0.1989 RANDOM 27.812
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] -0.42 -0.59 0.65 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.323 r_dihedral_angle_4_deg 17.444 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 6.303 r_scangle_it 3.645 r_scbond_it 2.473 r_angle_refined_deg 1.457 r_mcangle_it 1.338 r_mcbond_it 0.757 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.323 r_dihedral_angle_4_deg 17.444 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 6.303 r_scangle_it 3.645 r_scbond_it 2.473 r_angle_refined_deg 1.457 r_mcangle_it 1.338 r_mcbond_it 0.757 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1891 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 27
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling