8P7Q

The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8P7F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72931.5M (NH4)2SO4 17% Glycerol 0.1M Tris pH=7.0
Crystal Properties
Matthews coefficientSolvent content
3.1560.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.56α = 90
b = 69.56β = 90
c = 186.64γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.541

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.7734.899.920.024130.99918.972045349
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.870.09780.9746.41

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.7734.843061228599.90.1580.1570.186RANDOM17.59
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]
0.330.33-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.232
r_dihedral_angle_4_deg17.677
r_dihedral_angle_3_deg11.566
r_dihedral_angle_1_deg7.188
r_long_range_B_refined5.412
r_long_range_B_other5.135
r_scangle_other4.076
r_scbond_it2.882
r_scbond_other2.795
r_mcangle_other2.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.232
r_dihedral_angle_4_deg17.677
r_dihedral_angle_3_deg11.566
r_dihedral_angle_1_deg7.188
r_long_range_B_refined5.412
r_long_range_B_other5.135
r_scangle_other4.076
r_scbond_it2.882
r_scbond_other2.795
r_mcangle_other2.185
r_mcangle_it2.179
r_angle_refined_deg1.992
r_angle_other_deg1.691
r_mcbond_it1.53
r_mcbond_other1.53
r_chiral_restr0.169
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2490
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing