5LQ8

1.52 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with methylphosphonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LQ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82900.1 M MMT (DL-malic acid, MES and Tris base) buffer pH 8.0 and 25% (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.141.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.86α = 90
b = 57.08β = 106.56
c = 54.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.97951DiamondI24

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
11.5244970.0210.99716.22.240089
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)
11.521.5590.40.4310.6791.21.8

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 REPLACEMENTTHROUGHOUT5LQ51.524438156191996.950.159970.157590.20707RANDOM37.022
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]
0.17-2.461.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.696
r_sphericity_bonded31.78
r_sphericity_free20.86
r_dihedral_angle_4_deg16.809
r_dihedral_angle_3_deg14.46
r_scbond_other11.302
r_scbond_it11.294
r_scangle_other10.552
r_rigid_bond_restr10.184
r_long_range_B_other8.912
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.696
r_sphericity_bonded31.78
r_sphericity_free20.86
r_dihedral_angle_4_deg16.809
r_dihedral_angle_3_deg14.46
r_scbond_other11.302
r_scbond_it11.294
r_scangle_other10.552
r_rigid_bond_restr10.184
r_long_range_B_other8.912
r_long_range_B_refined8.883
r_mcangle_other7.974
r_mcangle_it7.946
r_mcbond_it7.577
r_mcbond_other7.537
r_dihedral_angle_1_deg6.15
r_angle_refined_deg1.519
r_angle_other_deg1.322
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2187
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing