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Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1 ERAP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.4M KCITRATE, 100 MM CACODYLATE (PH 5.7), 170 MM N-DODECYL-BETA-MALTOSIDE
Crystal Properties Matthews coefficient Solvent content 3.08 60.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.948 α = 90 b = 200.948 β = 90 c = 114.222 γ = 120
Symmetry Space Group P 6 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2010-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.7 30 99.6 0.2 12.3 12.2 37682 -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 2.7 2.85 99.7 0.96 3.2 12.5
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 MIR THROUGHOUT NONE 2.7 19.94 35800 1880 99.55 0.15496 0.15182 0.1809 0.21529 0.2306 RANDOM 13.501
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] -1.34 -0.67 -1.34 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.54 r_dihedral_angle_4_deg 18.267 r_dihedral_angle_3_deg 16.085 r_scangle_it 10.089 r_scbond_it 7.844 r_dihedral_angle_1_deg 6.583 r_mcangle_it 4.285 r_mcbond_it 2.607 r_angle_refined_deg 1.668 r_angle_other_deg 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.54 r_dihedral_angle_4_deg 18.267 r_dihedral_angle_3_deg 16.085 r_scangle_it 10.089 r_scbond_it 7.844 r_dihedral_angle_1_deg 6.583 r_mcangle_it 4.285 r_mcbond_it 2.607 r_angle_refined_deg 1.668 r_angle_other_deg 1.23 r_mcbond_other 0.714 r_chiral_restr 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6838 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling SHARP phasing