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Crystal structure of the NK2 fragment (28-289) of human hepatocyte growth factor/scatter factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NK1 PDB entry 1NK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 50 mM Ammonium sulfate, 17-23% PEG 2000 or 4000, 100 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, 0.5 mM Beta-octyl glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.15 α = 90 b = 48.15 β = 90 c = 461.673 γ = 120
Symmetry Space Group P 65 2 2
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 MARMOSAIC 300 mm CCD 2008-12-17 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-12-17 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-03-05 M SINGLE WAVELENGTH 4 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12700 APS 21-ID-D 2 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12700 APS 21-ID-D 3 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97860 APS 21-ID-G 4 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07800 APS 21-ID-D
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 1,2,3,4 2.4 50 93.7 0.134 0.134 9.3 6.4 13803 13803
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.44 74.3 0.447 0.447 1.1 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1NK1 2.6 41.52 13740 10223 1028 100 0.26952 0.26268 0.2579 0.33296 0.3317 RANDOM 37.752
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] 0.18 0.09 0.18 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.406 r_dihedral_angle_3_deg 15.433 r_dihedral_angle_4_deg 13.82 r_dihedral_angle_1_deg 4.58 r_angle_refined_deg 0.867 r_scangle_it 0.542 r_mcangle_it 0.367 r_scbond_it 0.301 r_mcbond_it 0.199 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.406 r_dihedral_angle_3_deg 15.433 r_dihedral_angle_4_deg 13.82 r_dihedral_angle_1_deg 4.58 r_angle_refined_deg 0.867 r_scangle_it 0.542 r_mcangle_it 0.367 r_scbond_it 0.301 r_mcbond_it 0.199 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2089 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data reduction MOSFLM data reduction HKL-2000 data scaling SCALA data scaling PHASER phasing