6Z28

Carboxypeptidase T mutant L254N with N-sulfamoyl-L-glutamic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QNV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1COUNTER-DIFFUSION2931.4 SA

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.52α = 90
b = 158.52β = 90
c = 104.871γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS 6M2018-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.8SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim 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
12.33099.340.2280.2382.410710.6134712
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4296.220.330.3842.3

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 REPLACEMENTTHROUGHOUT3QNV2.329.9632923174299.090.15960.15810.1881RANDOM17.962
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]
-0.02-0.01-0.020.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.634
r_dihedral_angle_4_deg19.166
r_dihedral_angle_3_deg13.795
r_dihedral_angle_1_deg7.741
r_angle_refined_deg1.795
r_angle_other_deg1.493
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.634
r_dihedral_angle_4_deg19.166
r_dihedral_angle_3_deg13.795
r_dihedral_angle_1_deg7.741
r_angle_refined_deg1.795
r_angle_other_deg1.493
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2581
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms29

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing