3LB5

Crystal structure of Hit-like protein involved in cell-cycle regulation from Bartonella henselae with unknown ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IMIPDB ENTRY 3imi

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6289PACT screen condition B8, 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20% PEG 6000, 25% EG as cryo-protectant; crystal tracking ID 202910b8; tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.71α = 90
b = 97.92β = 90
c = 111.85γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-12-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.92099.10.07517.36675981-326.426
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)
11.91.9594.40.4982.32.95338

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 3imi1.919.4739631198299.280.1840.1820.237RANDOM12.896
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]
-0.34-0.350.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.341
r_dihedral_angle_4_deg14.209
r_dihedral_angle_3_deg12.26
r_dihedral_angle_1_deg6.022
r_scangle_it3.06
r_scbond_it1.926
r_angle_refined_deg1.325
r_mcangle_it1.07
r_mcbond_it0.609
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.341
r_dihedral_angle_4_deg14.209
r_dihedral_angle_3_deg12.26
r_dihedral_angle_1_deg6.022
r_scangle_it3.06
r_scbond_it1.926
r_angle_refined_deg1.325
r_mcangle_it1.07
r_mcbond_it0.609
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4122
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms36

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction