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Crystal Structure of B-form Bombyx mori Pheromone Binding Protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GM0 pdb entry 1GM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 NaF, PEG 3350, pH 7.5, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.24 α = 90 b = 70.79 β = 90 c = 75.49 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 CCD 2002-06-05 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.950 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 43 91 12094 2 2
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 1GM0 2.3 43 13439 12080 605 89.89 0.222 0.22 0.22 0.2164 0.27 0.2692 RANDOM 26.569
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] -0.23 2.59 -2.36
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.05 r_dihedral_angle_1_deg 5.562 r_scbond_it 5.153 r_mcangle_it 4.414 r_angle_refined_deg 2.533 r_mcbond_it 2.324 r_angle_other_deg 1.133 r_symmetry_vdw_other 0.365 r_symmetry_vdw_refined 0.314 r_nbd_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.05 r_dihedral_angle_1_deg 5.562 r_scbond_it 5.153 r_mcangle_it 4.414 r_angle_refined_deg 2.533 r_mcbond_it 2.324 r_angle_other_deg 1.133 r_symmetry_vdw_other 0.365 r_symmetry_vdw_refined 0.314 r_nbd_other 0.25 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.216 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.174 r_nbtor_other 0.098 r_bond_refined_d 0.048 r_gen_planes_refined 0.015 r_gen_planes_other 0.013 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2166 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction