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Structure of NME1 covalently conjugated to imidazole fluorosulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 4.7 mg/mL solution protein-fluorosulfate conjugate combined with solution containing 0.2 M NaCl, 0.1 M HEPES pH 7.5 and 30% (v/v) PEG400 in sitting drops. Crystals frozen in LN2 stream without additional cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.462 α = 113.65 b = 68.058 β = 98.2 c = 69.682 γ = 112.46
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.75 59.81 96.7 0.128 0.101 0.99 7.7 2.6 22132 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.9 95.9 0.763 0.606 0.63 1.4 2.6
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 2HVE 2.75 59.81 20995 1134 96.65 0.19493 0.19338 0.1953 0.22314 0.2276 RANDOM 60.126
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] -3.02 1.15 0.17 -0.18 1.63 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.732 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_3_deg 13.804 r_dihedral_angle_1_deg 5.792 r_long_range_B_refined 5.501 r_long_range_B_other 5.496 r_scangle_other 3.644 r_mcangle_it 3.284 r_mcangle_other 3.284 r_scbond_it 2.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.732 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_3_deg 13.804 r_dihedral_angle_1_deg 5.792 r_long_range_B_refined 5.501 r_long_range_B_other 5.496 r_scangle_other 3.644 r_mcangle_it 3.284 r_mcangle_other 3.284 r_scbond_it 2.126 r_scbond_other 2.125 r_mcbond_it 1.985 r_mcbond_other 1.985 r_angle_refined_deg 1.202 r_angle_other_deg 1.183 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 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 7118 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing