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Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M MES pH 6.5, 1.6 M magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.54 α = 90 b = 74.09 β = 90 c = 155.81 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 100 PIXEL DECTRIS EIGER X 16M 2018-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 2.8 77.9 99.9 0.102 0.995 11.6 5.4 19083
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 2.8 2.95 99.9 0.412 0.904 5.3
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 1JKG 2.8 66.91 17130 1904 99.87 0.21705 0.21207 0.2145 0.26259 0.2626 RANDOM 40.085
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] 4.45 -2.68 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 23.525 r_dihedral_angle_3_deg 20.566 r_long_range_B_refined 7.426 r_long_range_B_other 7.425 r_dihedral_angle_1_deg 7.386 r_scangle_other 4.952 r_mcangle_it 4.63 r_mcangle_other 4.629 r_scbond_other 3.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 23.525 r_dihedral_angle_3_deg 20.566 r_long_range_B_refined 7.426 r_long_range_B_other 7.425 r_dihedral_angle_1_deg 7.386 r_scangle_other 4.952 r_mcangle_it 4.63 r_mcangle_other 4.629 r_scbond_other 3.053 r_scbond_it 3.052 r_mcbond_it 2.862 r_mcbond_other 2.862 r_angle_refined_deg 1.565 r_angle_other_deg 1.285 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 5101 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MOSFLM data reduction SCALA data scaling PHASER phasing