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Crystal structure of the open state of human endoplasmic reticulum aminopeptidase 1 ERAP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1M HEPES pH 7.5; 25% PEG 3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.246 α = 90 b = 132.816 β = 90 c = 233.687 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 PSI PILATUS 6M 2010-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 Diamond I24
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 3 30 97.8 0.153 5.8 3 60032 60032 -3 -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 3 3.16 98.8 0.668 1.6 3 8778
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2XDT 3 19.99 60032 56650 3019 97.57 0.23133 0.23133 0.22857 0.2275 0.28264 0.2778 RANDOM 34.252
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] 3.32 -1.74 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.351 r_dihedral_angle_4_deg 17.299 r_dihedral_angle_3_deg 15.324 r_scangle_it 7.851 r_dihedral_angle_1_deg 5.941 r_scbond_it 5.549 r_mcangle_it 3.888 r_mcbond_it 2.109 r_angle_refined_deg 1.087 r_angle_other_deg 0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.351 r_dihedral_angle_4_deg 17.299 r_dihedral_angle_3_deg 15.324 r_scangle_it 7.851 r_dihedral_angle_1_deg 5.941 r_scbond_it 5.549 r_mcangle_it 3.888 r_mcbond_it 2.109 r_angle_refined_deg 1.087 r_angle_other_deg 0.834 r_mcbond_other 0.314 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17494 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 109
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling