3MKP

Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BHTPDB ENTRY 1BHT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.243M Ammonium Sulfate, 22.295% PEG 3350, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9458.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.73α = 90
b = 129.73β = 90
c = 118.19γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9763ESRFID29

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
12.85099.70.0830.0838.97.925301252252.561.7
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)RedundancyNumber Unique Reflections (All)
2.82.8799.90.4980.4987.91661

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 1BHT2.8149.692396023907128799.780.2020.2020.1990.261RANDOM26.405
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]
-0.08-0.080.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_dihedral_angle_3_deg18.451
r_dihedral_angle_4_deg18.211
r_dihedral_angle_1_deg6.449
r_scangle_it4.14
r_mcangle_it3.311
r_scbond_it2.692
r_mcbond_it2.12
r_angle_refined_deg1.288
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.102
r_dihedral_angle_3_deg18.451
r_dihedral_angle_4_deg18.211
r_dihedral_angle_1_deg6.449
r_scangle_it4.14
r_mcangle_it3.311
r_scbond_it2.692
r_mcbond_it2.12
r_angle_refined_deg1.288
r_nbtor_refined0.314
r_symmetry_vdw_refined0.277
r_nbd_refined0.214
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.131
r_chiral_restr0.089
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5461
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms204

Software

Software
Software NamePurpose
MxCuBEdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling