4MDB

Structure of Mos1 transposase catalytic domain and Raltegravir with Mg


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F7TPDB ENTRY 2F7T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829022% w/v PEG4000, 100 mM Tris, pH 6.8, 5 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.8834.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.24α = 90
b = 44.24β = 90
c = 206.28γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.744.299.70.06514.55.5236102353922
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.899.90.3024.7

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 2F7T1.743.292357422263119899.520.199280.196990.24076RANDOM25.688
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]
-0.55-0.551.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.906
r_dihedral_angle_3_deg15.896
r_dihedral_angle_4_deg15.525
r_dihedral_angle_1_deg5.799
r_mcangle_it4.018
r_scbond_it3.417
r_mcbond_it2.638
r_mcbond_other2.633
r_angle_refined_deg2.09
r_angle_other_deg0.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.906
r_dihedral_angle_3_deg15.896
r_dihedral_angle_4_deg15.525
r_dihedral_angle_1_deg5.799
r_mcangle_it4.018
r_scbond_it3.417
r_mcbond_it2.638
r_mcbond_other2.633
r_angle_refined_deg2.09
r_angle_other_deg0.919
r_chiral_restr0.233
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms1711
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms34

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction