☰ Navigation Tabs
Crystal structure of a pheromone binding protein mutant D35N, from Apis mellifera, at pH 5.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H8V PDB ENTRY 2H8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.547 α = 90 b = 83.737 β = 90 c = 47.875 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate polar mirror 2008-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 30.36 98.4 0.056 0.056 16.5 3.6 7140 7140 45.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 99.8 0.39 0.39 3.1 3.6 1040
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2H8V 2.3 30 6435 6435 696 97.64 0.18098 0.18098 0.17746 0.21548 0.296 RANDOM 57.219
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] -0.3 1.61 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.206 r_dihedral_angle_3_deg 16.965 r_dihedral_angle_4_deg 10.932 r_dihedral_angle_1_deg 6.474 r_angle_refined_deg 1.94 r_scangle_it 1.813 r_angle_other_deg 1.436 r_scbond_it 1.326 r_mcangle_it 0.793 r_mcbond_it 0.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.206 r_dihedral_angle_3_deg 16.965 r_dihedral_angle_4_deg 10.932 r_dihedral_angle_1_deg 6.474 r_angle_refined_deg 1.94 r_scangle_it 1.813 r_angle_other_deg 1.436 r_scbond_it 1.326 r_mcangle_it 0.793 r_mcbond_it 0.618 r_symmetry_vdw_other 0.252 r_symmetry_hbond_refined 0.232 r_chiral_restr 0.23 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.205 r_nbd_other 0.19 r_nbtor_refined 0.182 r_mcbond_other 0.139 r_nbtor_other 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 907 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling REFMAC phasing