4LJ1

RipD (Rv1566c) from Mycobacterium tuberculosis: a non-catalytic NlpC/p60 domain protein with two penta-peptide repeat units (PVQQA-PVQPA)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.92930.1M Tris/HCl pH 7.9, 0.2M Trimethylamine N-oxide, 20% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1242.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.247α = 90
b = 30.752β = 120.85
c = 61.921γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
11.1753.1699.3439244361622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.171.6996.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.1753.16224392441701222199.320.147730.146720.16648RANDOM11.969
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]
-0.1-0.070.21-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.489
r_sphericity_free25.397
r_dihedral_angle_4_deg19.215
r_dihedral_angle_3_deg13.315
r_sphericity_bonded8.417
r_dihedral_angle_1_deg6.068
r_rigid_bond_restr3.105
r_angle_refined_deg1.441
r_angle_other_deg0.93
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.489
r_sphericity_free25.397
r_dihedral_angle_4_deg19.215
r_dihedral_angle_3_deg13.315
r_sphericity_bonded8.417
r_dihedral_angle_1_deg6.068
r_rigid_bond_restr3.105
r_angle_refined_deg1.441
r_angle_other_deg0.93
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms997
Nucleic Acid Atoms
Solvent Atoms139
Heterogen Atoms

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
SCALAdata scaling