1XKG

Crystal structure of the major house dust mite allergen Der p 1 in its pro form at 1.61 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6298PEG-4000, ammonium sulfate, sodium acetate, glycerol, yttrium chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.659α = 90
b = 66.557β = 90
c = 73.388γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCH2004-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.614099.60.05518.25.64150341444-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6796.90.4033978

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1YAL1.61404144441444208399.60.1540.1540.1530.186RANDOM24.2
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]
0.97-0.7-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.546
r_dihedral_angle_4_deg13.4
r_dihedral_angle_3_deg12.494
r_dihedral_angle_1_deg5.654
r_scangle_it3.798
r_scbond_it2.725
r_angle_refined_deg1.486
r_mcangle_it1.466
r_mcbond_it1.353
r_angle_other_deg0.809
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.546
r_dihedral_angle_4_deg13.4
r_dihedral_angle_3_deg12.494
r_dihedral_angle_1_deg5.654
r_scangle_it3.798
r_scbond_it2.725
r_angle_refined_deg1.486
r_mcangle_it1.466
r_mcbond_it1.353
r_angle_other_deg0.809
r_mcbond_other0.275
r_symmetry_vdw_other0.246
r_symmetry_vdw_refined0.232
r_nbd_refined0.217
r_nbtor_refined0.186
r_nbd_other0.185
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.145
r_chiral_restr0.09
r_nbtor_other0.083
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2375
Nucleic Acid Atoms
Solvent Atoms312
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
ARP/wARPmodel building