2YD0

Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1 ERAP1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.4M KCITRATE, 100 MM CACODYLATE (PH 5.7), 170 MM N-DODECYL-BETA-MALTOSIDE
Crystal Properties
Matthews coefficientSolvent content
3.0860.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 200.948α = 90
b = 200.948β = 90
c = 114.222γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2010-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.73099.60.212.312.237682-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8599.70.963.212.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUTNONE2.719.9435800188099.550.154960.151820.21529RANDOM13.501
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]
-1.34-0.67-1.342.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.54
r_dihedral_angle_4_deg18.267
r_dihedral_angle_3_deg16.085
r_scangle_it10.089
r_scbond_it7.844
r_dihedral_angle_1_deg6.583
r_mcangle_it4.285
r_mcbond_it2.607
r_angle_refined_deg1.668
r_angle_other_deg1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.54
r_dihedral_angle_4_deg18.267
r_dihedral_angle_3_deg16.085
r_scangle_it10.089
r_scbond_it7.844
r_dihedral_angle_1_deg6.583
r_mcangle_it4.285
r_mcbond_it2.607
r_angle_refined_deg1.668
r_angle_other_deg1.23
r_mcbond_other0.714
r_chiral_restr0.092
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms6838
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing