X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82942-4 microlitre of protein solution (5-15 mg/ml, 100 micromolar ThDP, 10 micromolar FAD, 1mM MgCl2 and 10 mM quinone Q0) were mixed with equal volume of reservoir solution (0.5% PEG6000, 0.5M NaCl, 40 mM DTT), pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 294.K
Crystal Properties
Matthews coefficientSolvent content
2.6954.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 188.18α = 90
b = 188.18β = 90
c = 249.4γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4BENT CRYSTAL2004-12-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.97897, 0.97946, 0.93929ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.75099.20.1010.0899.434.4122672-337.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.893.10.3470.282.762.21

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 DIFFRACTIONMADTHROUGHOUT2.720122207245399.90.220.2190.253RANDOM27.79
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]
-0.09-0.090.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.25
r_dihedral_angle_4_deg17.681
r_dihedral_angle_3_deg14.993
r_dihedral_angle_1_deg5.916
r_scangle_it1.463
r_angle_refined_deg1.229
r_scbond_it1.024
r_angle_other_deg0.79
r_mcbond_it0.524
r_mcangle_it0.504
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.25
r_dihedral_angle_4_deg17.681
r_dihedral_angle_3_deg14.993
r_dihedral_angle_1_deg5.916
r_scangle_it1.463
r_angle_refined_deg1.229
r_scbond_it1.024
r_angle_other_deg0.79
r_mcbond_it0.524
r_mcangle_it0.504
r_symmetry_vdw_other0.198
r_symmetry_vdw_refined0.19
r_nbd_refined0.184
r_nbtor_refined0.17
r_nbd_other0.169
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.127
r_nbtor_other0.081
r_mcbond_other0.065
r_chiral_restr0.064
r_xyhbond_nbd_other0.02
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms27180
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms548

Software

Software
Software NamePurpose
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction