3HMS

Crystal Crystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, orthorhombic crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NK1PDb entry 1NK1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829850 mM Ammonium sulfate, 28-32% PEG 1000 or 2000, 50 mM Tris-HCl pH 8.0, 5% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8232.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.91α = 90
b = 42.21β = 90
c = 52.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.99998APS32-ID

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.75099.60.0620.06232.76.89924992414.9
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)RedundancyNumber Unique Reflections (All)
1.71.7697.10.40.44.15.8971

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDb entry 1NK11.725.1199249610101096.70.2130.2020.2020.255RANDOM22
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]
-2.020.861.16
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d24.2
c_scangle_it3.33
c_mcangle_it2.37
c_scbond_it2.13
c_mcbond_it1.42
c_angle_deg1.2
c_improper_angle_d0.84
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms748
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms5

Software

Software
Software NamePurpose
COM-CATdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing