5ZHE

STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-981


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WYJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529520 % ETHYLENE GLYCOL, 2-5% PEG 35K
Crystal Properties
Matthews coefficientSolvent content
2.0941.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.713α = 90
b = 68.449β = 90
c = 109.253γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

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
12.182599.50.04418.46.325466
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)
12.182.2697.60.2652435

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 REPLACEMENTTHROUGHOUT3WYJ2.182524247116699.30.205860.203090.26308RANDOM52.869
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]
-1.361.30.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.53
r_dihedral_angle_4_deg24.892
r_dihedral_angle_3_deg19.36
r_long_range_B_refined13.56
r_long_range_B_other13.559
r_scangle_other10.506
r_mcangle_it7.893
r_mcangle_other7.891
r_scbond_it7.421
r_scbond_other7.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.53
r_dihedral_angle_4_deg24.892
r_dihedral_angle_3_deg19.36
r_long_range_B_refined13.56
r_long_range_B_other13.559
r_scangle_other10.506
r_mcangle_it7.893
r_mcangle_other7.891
r_scbond_it7.421
r_scbond_other7.393
r_dihedral_angle_1_deg6.653
r_mcbond_other6.048
r_mcbond_it6.047
r_angle_refined_deg1.728
r_angle_other_deg0.925
r_chiral_restr0.105
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3223
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing