7H6F | pdb_00007h6f

THE 1.25 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH 3-[2-(dimethylamino)-2-oxoethyl]-1-[(5-fluoro-1-benzothiophen-3-yl)methyl]indole-2-carboxylic acid (INDOLE 2-CARBOXYLIC ACID)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherapo structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.5293Sample of human Chymase in 50 mM MES/NaOH pH 5.5, 150mM NaCl, 1mM TCEP, 10% Glycerol) at a concentration of 11mg/ml to 14mg/ml.Add [2-[(4-methylpyridin-2-yl)amino]-2-oxoethyl] 2-methylquinoline-4-carboxylate at 10x molar ratio. The compound helps to obtain crystals but is not visible in the structures. Add 0.5 mM ZnCl2. Add inhibitor, incubate for 16h on ice. Crystallize using microbatch setups with Al's oil (Hampton Research), with total drop size 1ul with 50% protein sample, using crystallization reagent of 0.1M Tris/HCl pH 8.5, 0.2M NaCl, 25% PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.4750.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.87α = 90
b = 71.87β = 90
c = 47.95γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.003328SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.2519.9594.50.0680.07414.6963967
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3870.5790.64

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2519.9560731323394.490.145850.144440.15490.171950.1754RANDOM11.879
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]
-0.14-0.140.29
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined11.604
r_dihedral_angle_3_deg9.917
r_long_range_B_other9.757
r_dihedral_angle_1_deg7.143
r_dihedral_angle_2_deg6.034
r_scangle_other4.934
r_mcangle_other3.902
r_mcangle_it3.901
r_scbond_it3.378
r_scbond_other3.376
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined11.604
r_dihedral_angle_3_deg9.917
r_long_range_B_other9.757
r_dihedral_angle_1_deg7.143
r_dihedral_angle_2_deg6.034
r_scangle_other4.934
r_mcangle_other3.902
r_mcangle_it3.901
r_scbond_it3.378
r_scbond_other3.376
r_mcbond_it2.756
r_mcbond_other2.748
r_rigid_bond_restr2.664
r_angle_refined_deg1.996
r_angle_other_deg0.926
r_chiral_restr0.079
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.001
r_dihedral_angle_4_deg
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_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1759
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing