1PKV

The N-terminal domain of riboflavin synthase in complex with riboflavin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I8DPDB entry 1I8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729570 mM sodium potassium phosphate, pH 7.0, 100 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6353.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.161α = 90
b = 104.383β = 90
c = 85.113γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2000-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8424EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.62099.471717131
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.63100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1I8D2.619.77131679333799.460.176990.176990.174090.23469RANDOM38.393
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]
-1.582.17-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.087
r_scangle_it5.286
r_scbond_it3.216
r_mcangle_it2.151
r_angle_refined_deg1.798
r_mcbond_it1.068
r_symmetry_vdw_refined0.318
r_nbd_refined0.219
r_xyhbond_nbd_refined0.183
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.087
r_scangle_it5.286
r_scbond_it3.216
r_mcangle_it2.151
r_angle_refined_deg1.798
r_mcbond_it1.068
r_symmetry_vdw_refined0.318
r_nbd_refined0.219
r_xyhbond_nbd_refined0.183
r_chiral_restr0.112
r_bond_refined_d0.02
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1330
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing