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ERAP1 in the open conformation bound to 10mer phosphinic inhibitor DG014
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 293 Final drop composition: 100mM Tris pH 8.60, 3.5% PEG 8000, 3% D-sorbitol, 5mg/mL ERAP1 preincubated with inhibitor
Crystal Properties Matthews coefficient Solvent content 2.66 58.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.14 α = 90 b = 234.7 β = 93.12 c = 132.28 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 PIXEL DECTRIS PILATUS 6M 2014-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.100 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 2.83 87.73 99 0.182 4.1 2.7 80216 59.49
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 2.92 2.99 98.9 1.919 0.3 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3MDJ 2.92 56.06 1.34 60060 2987 81.7 0.201 0.198 0.1983 0.256 0.2553 Random selection 70.7
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 16.735 f_angle_d 0.78 f_chiral_restr 0.047 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20399 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 218
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction PHASER phasing STARANISO data scaling Aimless data scaling