5HQH

1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Protein from Listeria monocytogenes.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QDY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295Protein: 7.2 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3); Screen: Trap96 (D4), 0.2M NAD, 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
1.6224

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 22.577α = 90
b = 28.819β = 95.65
c = 59.733γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDC(111)2013-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.323099.80.050.0522.93.618244-314
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)
11.321.3499.30.5122.43.3

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 REPLACEMENTTHROUGHOUT4QDY1.3229.721726292699.840.163510.161980.1923RANDOM16.053
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]
0.320.4-0.580.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.305
r_dihedral_angle_4_deg15.235
r_dihedral_angle_3_deg10.391
r_long_range_B_refined6.676
r_long_range_B_other5.68
r_dihedral_angle_1_deg4.114
r_scangle_other1.892
r_angle_refined_deg1.561
r_scbond_other1.206
r_scbond_it1.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.305
r_dihedral_angle_4_deg15.235
r_dihedral_angle_3_deg10.391
r_long_range_B_refined6.676
r_long_range_B_other5.68
r_dihedral_angle_1_deg4.114
r_scangle_other1.892
r_angle_refined_deg1.561
r_scbond_other1.206
r_scbond_it1.204
r_mcangle_it1.188
r_mcangle_other1.187
r_angle_other_deg0.829
r_mcbond_other0.743
r_mcbond_it0.742
r_chiral_restr0.086
r_gen_planes_refined0.024
r_gen_planes_other0.02
r_bond_refined_d0.012
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms743
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing