3A3B

Crystal structure of LumP complexed with flavin mononucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DDYPDB ENTRY 3DDY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529320% (w/v) PEG 4000, 0.2M MgCl2, 100mM Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1242.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.858α = 90
b = 47.087β = 90
c = 160.923γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102008-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00Photon FactoryAR-NW12A

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
1233.2299.068722183

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 3DDY233.2222183249699.070.202260.196130.25523RANDOM25.7
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.86
r_dihedral_angle_3_deg17.855
r_dihedral_angle_4_deg17.674
r_dihedral_angle_1_deg10.693
r_scangle_it4.553
r_scbond_it2.821
r_mcangle_it2.168
r_angle_refined_deg1.904
r_mcbond_it1.319
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.86
r_dihedral_angle_3_deg17.855
r_dihedral_angle_4_deg17.674
r_dihedral_angle_1_deg10.693
r_scangle_it4.553
r_scbond_it2.821
r_mcangle_it2.168
r_angle_refined_deg1.904
r_mcbond_it1.319
r_nbtor_refined0.317
r_symmetry_vdw_refined0.241
r_nbd_refined0.213
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.165
r_chiral_restr0.158
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2711
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement