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X-ray crystal structure of the dimeric BMP antagonist NBL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 MES/imidazole (pH 6.5) and 0.02M of several amino acids (sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine)
Crystal Properties Matthews coefficient Solvent content 2.55 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.665 α = 90 b = 59.665 β = 90 c = 145.018 γ = 90
Symmetry Space Group P 41 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 80 CCD MARMOSAIC 300 mm CCD 2013-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.979 APS 21-ID-D
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 2.5 55.18 99.68 23.5 12.3 9690
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.5 55.18 8674 964 99.68 0.22175 0.21576 0.2202 0.27315 0.2733 RANDOM 89.054
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] 0.25 0.25 -0.49
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 43.6 r_dihedral_angle_2_deg 35.874 r_long_range_B_refined 16.68 r_long_range_B_other 16.676 r_dihedral_angle_3_deg 15.946 r_scangle_other 15.747 r_scbond_it 12.385 r_scbond_other 12.152 r_dihedral_angle_4_deg 10.462 r_mcangle_it 9.017
RMS Deviations Key Refinement Restraint Deviation r_sphericity_bonded 43.6 r_dihedral_angle_2_deg 35.874 r_long_range_B_refined 16.68 r_long_range_B_other 16.676 r_dihedral_angle_3_deg 15.946 r_scangle_other 15.747 r_scbond_it 12.385 r_scbond_other 12.152 r_dihedral_angle_4_deg 10.462 r_mcangle_it 9.017 r_mcangle_other 9.013 r_mcbond_it 6.921 r_mcbond_other 6.921 r_dihedral_angle_1_deg 6.8 r_rigid_bond_restr 3.331 r_angle_refined_deg 1.523 r_angle_other_deg 1.011 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1330 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing