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Crystal structure of a pheromone binding protein mutant D35A, from Apis mellifera, at pH 7.0
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 7 293 2.1M ammonium sulfate, 0.2M di-ammonium phosphate, 20mM di-sodium phosphate, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.873 α = 90 b = 60.859 β = 90 c = 56.682 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MAR scanner 345 mm plate polar mirror 2008-01-14 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 2.01 30.43 97.4 0.057 0.057 22.2 6.2 14418 14418 21.84
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) 2.01 2.12 82.2 0.254 0.254 6.4 5.9 10192
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 2H8V 2.03 20 13343 13343 1031 99.5 0.17535 0.17535 0.17166 0.2117 0.22409 0.2563 RANDOM 27.559
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] 1.13 -1.58 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.863 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 13.283 r_dihedral_angle_1_deg 9.444 r_scangle_it 2.781 r_scbond_it 1.989 r_angle_refined_deg 1.375 r_mcbond_it 1.078 r_mcangle_it 1.029 r_angle_other_deg 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.863 r_dihedral_angle_4_deg 22.622 r_dihedral_angle_3_deg 13.283 r_dihedral_angle_1_deg 9.444 r_scangle_it 2.781 r_scbond_it 1.989 r_angle_refined_deg 1.375 r_mcbond_it 1.078 r_mcangle_it 1.029 r_angle_other_deg 0.982 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.214 r_nbd_other 0.197 r_symmetry_hbond_refined 0.188 r_mcbond_other 0.186 r_symmetry_vdw_other 0.184 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.178 r_chiral_restr 0.095 r_nbtor_other 0.09 r_bond_refined_d 0.013 r_bond_other_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1846 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection MOSFLM data reduction SCALA data scaling MOLREP phasing