5LQ5

1.46 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with phosphite


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82900.1 M SPG (succinic acid, sodium dihydrogen phosphate, glycine) buffer pH 8.0 and 25% (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1643.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.33α = 90
b = 57.61β = 107.15
c = 54.79γ = 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
11.4644.2797.30.0210.99915.83.546137
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)
11.461.4978.40.670.5691.12.5

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 REPLACEMENTTHROUGHOUT5JVB1.4644.2744161224496.820.147640.145970.18RANDOM34.119
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]
0.02-1.471.46-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.938
r_sphericity_bonded30.611
r_sphericity_free22.292
r_dihedral_angle_3_deg14.837
r_dihedral_angle_4_deg13.947
r_scbond_other11.529
r_scbond_it11.519
r_scangle_other9.923
r_rigid_bond_restr9.18
r_long_range_B_other7.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.938
r_sphericity_bonded30.611
r_sphericity_free22.292
r_dihedral_angle_3_deg14.837
r_dihedral_angle_4_deg13.947
r_scbond_other11.529
r_scbond_it11.519
r_scangle_other9.923
r_rigid_bond_restr9.18
r_long_range_B_other7.758
r_long_range_B_refined7.716
r_dihedral_angle_1_deg5.937
r_mcbond_it4.433
r_mcangle_other4.373
r_mcangle_it4.229
r_mcbond_other3.679
r_angle_refined_deg1.468
r_angle_other_deg1.338
r_chiral_restr0.169
r_bond_refined_d0.013
r_gen_planes_refined0.008
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 Atoms2206
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building