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Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BHT PDB ENTRY 1BHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.243M Ammonium Sulfate, 22.295% PEG 3350, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.94 58.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.73 α = 90 b = 129.73 β = 90 c = 118.19 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 100 CCD ADSC QUANTUM 315 2007-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 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 2.8 50 99.7 0.083 0.083 8.9 7.9 25301 25225 2.5 61.7
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) 2.8 2.87 99.9 0.498 0.498 7.9 1661
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BHT 2.81 49.69 23960 23907 1287 99.78 0.202 0.202 0.199 0.261 0.2628 RANDOM 26.405
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] -0.08 -0.08 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_dihedral_angle_3_deg 18.451 r_dihedral_angle_4_deg 18.211 r_dihedral_angle_1_deg 6.449 r_scangle_it 4.14 r_mcangle_it 3.311 r_scbond_it 2.692 r_mcbond_it 2.12 r_angle_refined_deg 1.288 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.102 r_dihedral_angle_3_deg 18.451 r_dihedral_angle_4_deg 18.211 r_dihedral_angle_1_deg 6.449 r_scangle_it 4.14 r_mcangle_it 3.311 r_scbond_it 2.692 r_mcbond_it 2.12 r_angle_refined_deg 1.288 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5461 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 204
Software Software Software Name Purpose MxCuBE data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling