6S1W

Crystal structure of dimeric M-PMV protease D26N mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6292Protein solution: 4.1 mg/mL protein, 5 mM TCEP, 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M sodium citrate buffer, 15% propan-2-ol, 5 mM TCEP;
Crystal Properties
Matthew coefficientSolvent content
2.3748.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.987α = 90
b = 29.571β = 102.52
c = 85.2γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.9848.9198.90.1190.1390.9978.243.621712325
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.194.30.6270.7370.5212.033.4

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 REPLACEMENTFREE R-VALUE6S1U, chain A1.9848.816122100098.90.203130.199560.26063RANDOM34.024
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]
3.180.22-2.45-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.09
r_dihedral_angle_3_deg16.612
r_dihedral_angle_4_deg14.287
r_dihedral_angle_1_deg8.13
r_long_range_B_refined6.31
r_long_range_B_other6.257
r_scangle_other3.085
r_mcangle_other2.991
r_mcangle_it2.988
r_scbond_it1.977
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.09
r_dihedral_angle_3_deg16.612
r_dihedral_angle_4_deg14.287
r_dihedral_angle_1_deg8.13
r_long_range_B_refined6.31
r_long_range_B_other6.257
r_scangle_other3.085
r_mcangle_other2.991
r_mcangle_it2.988
r_scbond_it1.977
r_scbond_other1.976
r_angle_refined_deg1.839
r_mcbond_it1.826
r_mcbond_other1.809
r_angle_other_deg1.385
r_chiral_restr0.095
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1648
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement