4MSM

Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.2M Ammonium Phosphate dibasic, 20%w/v PEG 3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.017α = 90
b = 95.322β = 90
c = 112.944γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2013-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.74501000.1160.11626.35.863915630132.762.76
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.78100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4K1R1.7472.856390859814319898.590.196470.194930.22546RANDOM25.735
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]
0.04-0.110.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.035
r_dihedral_angle_3_deg14.237
r_dihedral_angle_4_deg12.464
r_dihedral_angle_1_deg6.342
r_scbond_it3.138
r_mcangle_it3.062
r_mcbond_it2.273
r_mcbond_other2.273
r_angle_refined_deg2.063
r_angle_other_deg0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.035
r_dihedral_angle_3_deg14.237
r_dihedral_angle_4_deg12.464
r_dihedral_angle_1_deg6.342
r_scbond_it3.138
r_mcangle_it3.062
r_mcbond_it2.273
r_mcbond_other2.273
r_angle_refined_deg2.063
r_angle_other_deg0.89
r_chiral_restr0.124
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4124
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection