2VBV

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% W/V PEG 8000, 200 MM SODIUM IODIDE
Crystal Properties
Matthews coefficientSolvent content
2.652.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.482α = 90
b = 73.299β = 90
c = 104.907γ = 90
Symmetry
Space GroupP 21 21 21

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
12.438.5898.60.138.675.512903
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)
12.42.5598.50.692.255.62

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 2VBT2.420122026441000.2320.2270.323RANDOM42.39
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]
0.842.41-3.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.186
r_dihedral_angle_3_deg20.516
r_dihedral_angle_4_deg14.065
r_dihedral_angle_1_deg8.057
r_angle_other_deg4.036
r_scangle_it2.951
r_scbond_it1.814
r_angle_refined_deg1.7
r_mcangle_it1.406
r_mcbond_it0.757
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.186
r_dihedral_angle_3_deg20.516
r_dihedral_angle_4_deg14.065
r_dihedral_angle_1_deg8.057
r_angle_other_deg4.036
r_scangle_it2.951
r_scbond_it1.814
r_angle_refined_deg1.7
r_mcangle_it1.406
r_mcbond_it0.757
r_nbd_other0.23
r_nbd_refined0.225
r_xyhbond_nbd_refined0.223
r_symmetry_vdw_other0.209
r_nbtor_refined0.196
r_symmetry_vdw_refined0.184
r_nbtor_other0.114
r_symmetry_hbond_refined0.102
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_other0.007
r_gen_planes_refined0.005
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 Atoms2178
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing