6A8O

Crystal structures of the serine protease domain of murine plasma kallikrein with peptide inhibitor mupain-1-16


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ANY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29825% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9558.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.26α = 90
b = 82.45β = 90
c = 105.32γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9791SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.7752.6699.80.090.0390.99815.73716315
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.772.8799.80.0915.73

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 REPLACEMENTTHROUGHOUT2ANY2.7752.661550181499.80.2170.2120.3RANDOM69.17
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]
-22.53-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.563
r_dihedral_angle_3_deg19.429
r_dihedral_angle_4_deg19.354
r_long_range_B_refined14.357
r_long_range_B_other14.355
r_scangle_other10.921
r_mcangle_other9.555
r_mcangle_it9.554
r_dihedral_angle_1_deg8.5
r_scbond_it7.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.563
r_dihedral_angle_3_deg19.429
r_dihedral_angle_4_deg19.354
r_long_range_B_refined14.357
r_long_range_B_other14.355
r_scangle_other10.921
r_mcangle_other9.555
r_mcangle_it9.554
r_dihedral_angle_1_deg8.5
r_scbond_it7.175
r_scbond_other7.173
r_mcbond_it6.318
r_mcbond_other6.302
r_angle_refined_deg1.642
r_angle_other_deg1.207
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3799
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling