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Structure of OBP1 from Varroa destructor, form P2<1>
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NYJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 2/3 of the initial crystallization conditions (CHES pH9.5, 0.1M, 30% PEG3000 w/v ) and 1/3 of ammonium sulfate screen (0.2 M sodium nitrate, 2.2M ammonium sulfate).
Crystal Properties Matthews coefficient Solvent content 2.23 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.604 α = 90 b = 112.959 β = 98.95 c = 41.817 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.199 40.1 97.2 0.065 0.998 13.15 7 87891
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.27 91.4 0.885 0.788 1.19 6.4
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 7NYJ 1.199 38.83 83470 4402 97.23 0.18056 0.17947 0.1802 0.20145 0.2012 RANDOM 19.045
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] 0.01 0.01 -0.09 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.984 r_dihedral_angle_4_deg 18.367 r_dihedral_angle_3_deg 11.984 r_dihedral_angle_1_deg 5.433 r_long_range_B_refined 4.713 r_long_range_B_other 4.66 r_scangle_other 3.448 r_scbond_it 2.349 r_scbond_other 2.348 r_angle_refined_deg 2.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.984 r_dihedral_angle_4_deg 18.367 r_dihedral_angle_3_deg 11.984 r_dihedral_angle_1_deg 5.433 r_long_range_B_refined 4.713 r_long_range_B_other 4.66 r_scangle_other 3.448 r_scbond_it 2.349 r_scbond_other 2.348 r_angle_refined_deg 2.197 r_angle_other_deg 1.725 r_mcangle_other 1.686 r_mcangle_it 1.685 r_mcbond_it 1.139 r_mcbond_other 1.136 r_chiral_restr 0.28 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2213 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing