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CCP5 in complex with Glu-P-peptide 1 transition state analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8V3M crystal structure of apo CCP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.429 α = 90 b = 81.372 β = 90 c = 104 γ = 90
Symmetry Space Group P 2 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 93 PIXEL DECTRIS EIGER X 9M 2022-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 34.55 100 0.175 0.187 0.998 13.8 14.3 25384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 1.455 1.56 0.712 2 14.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 34.55 1.34 25340 1187 99.97 0.2043 0.2031 0.2039 0.2269 0.228
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.252 f_angle_d 0.642 f_chiral_restr 0.04 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3765 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing