6TCX

Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9PAP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100 mM HEPES pH 7.5 and 80% 2-Methyl-2,4-pentanediol (MPD)
Crystal Properties
Matthews coefficientSolvent content
2.1843.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.644α = 90
b = 48.921β = 90
c = 101.547γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6550.6599.80.0260.99915.113.126295
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.680.2520.876

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE9PAP1.6544.11226239132599.7490.1980.19640.221424.649
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]
-0.3121.251-0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.326
r_dihedral_angle_4_deg15.895
r_dihedral_angle_other_3_deg12.97
r_dihedral_angle_3_deg10.435
r_dihedral_angle_1_deg6.009
r_lrange_other3.28
r_lrange_it3.277
r_scangle_it2.028
r_scangle_other2.027
r_mcangle_other1.503
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.326
r_dihedral_angle_4_deg15.895
r_dihedral_angle_other_3_deg12.97
r_dihedral_angle_3_deg10.435
r_dihedral_angle_1_deg6.009
r_lrange_other3.28
r_lrange_it3.277
r_scangle_it2.028
r_scangle_other2.027
r_mcangle_other1.503
r_mcangle_it1.501
r_scbond_it1.258
r_scbond_other1.258
r_angle_other_deg1.207
r_angle_refined_deg1.175
r_mcbond_it0.912
r_mcbond_other0.907
r_nbd_other0.188
r_nbd_refined0.173
r_nbtor_refined0.166
r_symmetry_nbd_other0.165
r_symmetry_xyhbond_nbd_refined0.135
r_xyhbond_nbd_refined0.103
r_symmetry_nbtor_other0.073
r_symmetry_nbd_refined0.067
r_chiral_restr0.05
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1636
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
autoXDSdata reduction
Aimlessdata scaling
MOLREPphasing