3PHQ

Crystal structure of S64-4 in complex with KDO


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1HANGING DROP8.5289Sodium citrate tribasic dihydrate, 2-propanol, PEG 4000, pH 8.5, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4449.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.84α = 90
b = 81.15β = 90
c = 94.19γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXISOSMIC BLUE MIRRORS2009-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0021.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1219.82698.431620

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 REPLACEMENTTHROUGHOUT219.7630005160598.330.229230.226850.27487RANDOM32.243
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]
0.060.07-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.027
r_dihedral_angle_4_deg14.269
r_dihedral_angle_3_deg13.205
r_dihedral_angle_1_deg6.094
r_scangle_it2.94
r_scbond_it1.891
r_mcangle_it1.269
r_angle_refined_deg1.18
r_mcbond_it0.673
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.027
r_dihedral_angle_4_deg14.269
r_dihedral_angle_3_deg13.205
r_dihedral_angle_1_deg6.094
r_scangle_it2.94
r_scbond_it1.891
r_mcangle_it1.269
r_angle_refined_deg1.18
r_mcbond_it0.673
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3274
Nucleic Acid Atoms
Solvent Atoms356
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
PHASERphasing
PHENIXrefinement