1TLQ

Crystal structure of protein ypjQ from Bacillus subtilis, Pfam DUF64


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherExperimental electron density from Selenium SAD experiment.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.7529126% Peg 4k, 0.1M Tris, 0.8M Lithium Chloride, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.1260.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.112α = 90
b = 118.112β = 90
c = 65.792γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9A0.98NSLSX9A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.42099.80.07431.7511.152005020050
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4999.90.4564.451998

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 DIFFRACTIONSADTHROUGHOUTExperimental electron density from Selenium SAD experiment.2.4201047052999.590.235340.232440.29466RANDOM44.966
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]
2.581.292.58-3.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.527
r_scangle_it7.926
r_scbond_it5.288
r_mcangle_it3.534
r_angle_refined_deg3.232
r_mcbond_it2.034
r_nbd_refined0.312
r_metal_ion_refined0.283
r_symmetry_vdw_refined0.281
r_chiral_restr0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.527
r_scangle_it7.926
r_scbond_it5.288
r_mcangle_it3.534
r_angle_refined_deg3.232
r_mcbond_it2.034
r_nbd_refined0.312
r_metal_ion_refined0.283
r_symmetry_vdw_refined0.281
r_chiral_restr0.238
r_symmetry_hbond_refined0.234
r_xyhbond_nbd_refined0.187
r_bond_refined_d0.046
r_gen_planes_refined0.019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1262
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing