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The structure of the NK1 fragment of HGF/SF complexed with 2FA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 19% PEG 4000, 200 mM Na Acetate, 150 mM Tris
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.225 α = 90 b = 63.078 β = 95.06 c = 57.275 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 CCD ADSC QUANTUM 315 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.981 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 30 99.8 0.055 0.055 16.1 3.5 25692
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.2 99.8 0.398 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 1NK1 2 26.51 24374 1303 99.59 0.207 0.205 0.2034 0.251 0.2471 RANDOM 37.006
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 19.113 r_dihedral_angle_3_deg 15.801 r_dihedral_angle_1_deg 6.421 r_scangle_it 4.308 r_mcangle_it 3.51 r_scbond_it 2.957 r_mcbond_it 2.533 r_angle_refined_deg 1.235 r_symmetry_hbond_refined 0.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.012 r_dihedral_angle_4_deg 19.113 r_dihedral_angle_3_deg 15.801 r_dihedral_angle_1_deg 6.421 r_scangle_it 4.308 r_mcangle_it 3.51 r_scbond_it 2.957 r_mcbond_it 2.533 r_angle_refined_deg 1.235 r_symmetry_hbond_refined 0.404 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2774 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing