5NX0

Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at room temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LWO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.22772.0 M K2HPO4/NAH2PO4, 250 MM NACL, 0.04 % AZIDE, 20 MM DITHIODIETHANOL, PH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.8156.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.075α = 90
b = 61.075β = 90
c = 97.066γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHOSMIC MIRRORS2016-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.80352.89980.035010.9913.921.81943225.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8031.868920.51920.6251.121.6

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 REPLACEMENTTHROUGHOUT5LWO1.80352.891847695697.580.160440.158120.20853RANDOM29.551
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]
0.040.020.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.169
r_dihedral_angle_4_deg15.558
r_dihedral_angle_3_deg13.109
r_long_range_B_refined8.393
r_long_range_B_other8.267
r_scangle_other6.788
r_dihedral_angle_1_deg5.604
r_scbond_it4.395
r_scbond_other4.385
r_mcangle_other3.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.169
r_dihedral_angle_4_deg15.558
r_dihedral_angle_3_deg13.109
r_long_range_B_refined8.393
r_long_range_B_other8.267
r_scangle_other6.788
r_dihedral_angle_1_deg5.604
r_scbond_it4.395
r_scbond_other4.385
r_mcangle_other3.609
r_mcangle_it3.606
r_mcbond_it2.67
r_mcbond_other2.646
r_angle_refined_deg1.879
r_angle_other_deg1.066
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms1303
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing