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Crystal structure of Pru du amandin, an allergenic protein from prunus dulcis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UD1 PDB ENTRY 1UD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris-HCl (pH8.5), 2.0M Ammonium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.099 α = 90 b = 151.099 β = 90 c = 164.628 γ = 90
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 Osmic Mirrors 2006-03-07 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 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 3.2 50 96.6 0.137 4.1 2.56 59067 59067
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) 3.2 3.31 98.4 0.31 1.7 2.43
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UD1 3.2 33.31 43052 4859 78.65 0.25679 0.2543 0.2539 0.27899 0.2774 RANDOM 56.023
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] 2.88 2.88 -5.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.769 r_dihedral_angle_3_deg 20.706 r_dihedral_angle_4_deg 17.67 r_mcangle_it 11.989 r_mcbond_it 7.971 r_scangle_it 5.809 r_scbond_it 4.954 r_dihedral_angle_1_deg 1.949 r_angle_refined_deg 1.891 r_symmetry_vdw_refined 0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.769 r_dihedral_angle_3_deg 20.706 r_dihedral_angle_4_deg 17.67 r_mcangle_it 11.989 r_mcbond_it 7.971 r_scangle_it 5.809 r_scbond_it 4.954 r_dihedral_angle_1_deg 1.949 r_angle_refined_deg 1.891 r_symmetry_vdw_refined 0.358 r_nbtor_refined 0.343 r_nbd_refined 0.313 r_xyhbond_nbd_refined 0.189 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.128 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18252 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement AUTOMAR data reduction