X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VK4PDB entry 2VK4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.25281.152 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 30 seconds in 2 uL mother liquor + 2 uL 15% w/v glycerol, 200 mM acetaldehyde prior to flash freezing.
Crystal Properties
Matthews coefficientSolvent content
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.36α = 80.1
b = 78.48β = 67.72
c = 100.57γ = 77.4
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X121.00001EMBL/DESY, HAMBURGX12

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.0438.2593.20.0860.1090.0650.9968.62.712696424.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.0866.80.6590.8370.5080.6891.72.3

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 REPLACEMENTTHROUGHOUTPDB entry 2VK42.0438.2512599497093.150.221230.220690.2903RANDOM37.997
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]
-1.7-1.22-0.76-1.370.621.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.903
r_dihedral_angle_4_deg18.943
r_dihedral_angle_3_deg17.669
r_dihedral_angle_1_deg7.726
r_long_range_B_refined7.014
r_long_range_B_other7.014
r_scangle_other4.719
r_mcangle_it4.402
r_mcangle_other4.401
r_scbond_it3.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.903
r_dihedral_angle_4_deg18.943
r_dihedral_angle_3_deg17.669
r_dihedral_angle_1_deg7.726
r_long_range_B_refined7.014
r_long_range_B_other7.014
r_scangle_other4.719
r_mcangle_it4.402
r_mcangle_other4.401
r_scbond_it3.095
r_scbond_other3.095
r_mcbond_it2.98
r_mcbond_other2.98
r_angle_refined_deg1.422
r_angle_other_deg0.919
r_chiral_restr0.069
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms16531
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing