2VBU

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VBTPDB ENTRY 2VBT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
135% V/V MPD, 100 MM IMIDAZOLE
Crystal Properties
Matthews coefficientSolvent content
358.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.845α = 90
b = 104.845β = 90
c = 32.802γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.733.1599.80.0523.17.8220274
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)
11.71.899.40.474.356.3

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 2VBT1.720189499971000.1630.1610.212RANDOM22.19
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]
-0.6-0.61.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.208
r_dihedral_angle_3_deg14.808
r_scangle_it11.901
r_dihedral_angle_4_deg11.557
r_scbond_it8.221
r_dihedral_angle_1_deg5.712
r_mcangle_it5.493
r_angle_other_deg3.826
r_mcbond_it3.775
r_angle_refined_deg1.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.208
r_dihedral_angle_3_deg14.808
r_scangle_it11.901
r_dihedral_angle_4_deg11.557
r_scbond_it8.221
r_dihedral_angle_1_deg5.712
r_mcangle_it5.493
r_angle_other_deg3.826
r_mcbond_it3.775
r_angle_refined_deg1.551
r_symmetry_vdw_other0.261
r_nbd_other0.226
r_nbd_refined0.188
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.142
r_symmetry_vdw_refined0.118
r_nbtor_other0.115
r_symmetry_hbond_refined0.089
r_chiral_restr0.074
r_bond_refined_d0.012
r_gen_planes_other0.008
r_gen_planes_refined0.006
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1065
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing