7VM6

Crystal structure of uPA in complex with 6-amidino-2-naphthol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DVA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62982.0 M ammonium sulfate, 5% PEG 400, 20 mM sodium citrate, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.1342.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.435α = 90
b = 120.435β = 90
c = 42.637γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2018-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U11.0SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.7950980.0950.99612.578.221201
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.830.650.81

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DVA1.7930.131825698788.940.20390.20170.2429RANDOM22.507
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]
-0.16-0.08-0.160.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.422
r_dihedral_angle_4_deg18.289
r_dihedral_angle_3_deg16.938
r_dihedral_angle_1_deg7.578
r_angle_refined_deg1.288
r_angle_other_deg0.874
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.422
r_dihedral_angle_4_deg18.289
r_dihedral_angle_3_deg16.938
r_dihedral_angle_1_deg7.578
r_angle_refined_deg1.288
r_angle_other_deg0.874
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1952
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing