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Crystal structure of the major house dust mite allergen Der p 1 in its pro form at 1.61 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YAL PDB entry 1YAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 PEG-4000, ammonium sulfate, sodium acetate, glycerol, yttrium chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.659 α = 90 b = 66.557 β = 90 c = 73.388 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 120 IMAGE PLATE MARRESEARCH 2004-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.61 40 99.6 0.055 18.2 5.6 41503 41444 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.67 96.9 0.403 3978
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 PDB entry 1YAL 1.61 40 41444 41444 2083 99.6 0.154 0.154 0.153 0.1619 0.186 0.1959 RANDOM 24.2
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.546 r_dihedral_angle_4_deg 13.4 r_dihedral_angle_3_deg 12.494 r_dihedral_angle_1_deg 5.654 r_scangle_it 3.798 r_scbond_it 2.725 r_angle_refined_deg 1.486 r_mcangle_it 1.466 r_mcbond_it 1.353 r_angle_other_deg 0.809
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.546 r_dihedral_angle_4_deg 13.4 r_dihedral_angle_3_deg 12.494 r_dihedral_angle_1_deg 5.654 r_scangle_it 3.798 r_scbond_it 2.725 r_angle_refined_deg 1.486 r_mcangle_it 1.466 r_mcbond_it 1.353 r_angle_other_deg 0.809 r_mcbond_other 0.275 r_symmetry_vdw_other 0.246 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.217 r_nbtor_refined 0.186 r_nbd_other 0.185 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.09 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2375 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing ARP/wARP model building