2VBT

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and PO4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VBSPDB ENTRY 2VBS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
140% V/V ETHYLENE GLYCOL, 100 MM PHOSPHATE-CITRATE PH 4.2, 200 MM NH4SO4
Crystal Properties
Matthews coefficientSolvent content
5.376.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.72α = 90
b = 77.72β = 90
c = 106.868γ = 90
Symmetry
Space GroupP 43 21 2

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
12.738.3299.50.0816.575.59448
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)
12.72.8798.10.922.025.6

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 2VBS2.720897145399.70.2110.2090.266RANDOM60.53
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]
2.322.32-4.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.962
r_dihedral_angle_3_deg16.911
r_dihedral_angle_4_deg8.991
r_dihedral_angle_1_deg6.337
r_angle_other_deg3.937
r_scangle_it2.547
r_mcangle_it1.738
r_angle_refined_deg1.476
r_scbond_it1.464
r_mcbond_it0.932
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.962
r_dihedral_angle_3_deg16.911
r_dihedral_angle_4_deg8.991
r_dihedral_angle_1_deg6.337
r_angle_other_deg3.937
r_scangle_it2.547
r_mcangle_it1.738
r_angle_refined_deg1.476
r_scbond_it1.464
r_mcbond_it0.932
r_nbd_other0.225
r_symmetry_vdw_refined0.213
r_nbd_refined0.205
r_nbtor_refined0.191
r_symmetry_vdw_other0.16
r_xyhbond_nbd_refined0.151
r_nbtor_other0.111
r_chiral_restr0.079
r_bond_refined_d0.014
r_gen_planes_other0.005
r_gen_planes_refined0.004
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
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 Atoms1105
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing