4KH9

Crystal structure of a DUF4785 family protein (lpg0956) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.832930.2M calcium acetate, 10.0% polyethylene glycol 8000, 0.1M Imidazole pH 7.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.807α = 64.13
b = 62.975β = 82.94
c = 70.632γ = 67.17
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2013-01-24MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
1245.53788.30.04311.893.6647483-335.553
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)
122.0591.30.6551.16

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT245.53747471241091.50.19510.19370.2207RANDOM47.0454
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]
-1.65053.23431.38330.9560.44650.6945
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.82
t_other_torsion2.51
t_angle_deg1.1
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.82
t_other_torsion2.51
t_angle_deg1.1
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5743
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms26

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNTrefinement
XDSdata reduction
SHELXDphasing
BUSTERrefinement