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Crystal structure of the binding domain of Paraclostridial Mosquitocidal Protein 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 0.12 M Ethylene glycols, 0.1 M Buffer System 3 pH 8.5, 50 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)
Crystal Properties Matthews coefficient Solvent content 2.15 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.146 α = 90 b = 38.686 β = 116.74 c = 108.514 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2017-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.984 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 48.46 96.9 0.097 0.135 0.093 0.995 8.3 3.5 31355
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 94.4 0.725 1.009 0.7 0.641 1.6 3.3
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 4KBB 1.95 48.46 29725 1629 96.61 0.17756 0.17583 0.1849 0.2093 0.2155 RANDOM 33.866
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] 0.1 1.55 -0.53 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 16.366 r_dihedral_angle_3_deg 13.172 r_dihedral_angle_1_deg 7.151 r_long_range_B_refined 6.461 r_long_range_B_other 6.461 r_scangle_other 4.668 r_mcangle_it 3.614 r_mcangle_other 3.613 r_scbond_it 2.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.97 r_dihedral_angle_4_deg 16.366 r_dihedral_angle_3_deg 13.172 r_dihedral_angle_1_deg 7.151 r_long_range_B_refined 6.461 r_long_range_B_other 6.461 r_scangle_other 4.668 r_mcangle_it 3.614 r_mcangle_other 3.613 r_scbond_it 2.941 r_scbond_other 2.94 r_mcbond_it 2.358 r_mcbond_other 2.352 r_angle_refined_deg 1.206 r_angle_other_deg 0.839 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 3503 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MoRDa phasing