☰ Navigation Tabs
Crystal structure of human odorant binding protein OBPIIa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 Protein solution: 14 mg/ml protein, 0.2 M imidazole, 0.4 M NaCl, 10 mM Tris-HCl, 1.3 mM Menthol, 3.3 %(v/v) Methanol;
Reservoir solution: 20 %(w/v) PEG 3350, 0.1 M ammonium citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.949 α = 90 b = 52.949 β = 90 c = 232.098 γ = 90
Symmetry Space Group P 41 21 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 MARMOSAIC 225 mm CCD MIRRORS 2011-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 2.6 35 99.7 0.049 31.88 8.8 10926 10926 -3 -3 63.91
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 2.6 2.7 97.5 0.645 2.76
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 3EYC 2.6 33.7 10926 10926 523 99.64 0.2373 0.2373 0.235 0.2362 0.2844 0.2881 RANDOM 75.6
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] -0.92 -0.92 1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.553 r_dihedral_angle_4_deg 20.701 r_dihedral_angle_3_deg 15.354 r_dihedral_angle_1_deg 6.52 r_mcangle_it 3.74 r_mcbond_it 2.16 r_mcbond_other 2.16 r_angle_refined_deg 1.309 r_angle_other_deg 0.908 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.553 r_dihedral_angle_4_deg 20.701 r_dihedral_angle_3_deg 15.354 r_dihedral_angle_1_deg 6.52 r_mcangle_it 3.74 r_mcbond_it 2.16 r_mcbond_other 2.16 r_angle_refined_deg 1.309 r_angle_other_deg 0.908 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction PHASER phasing