9H87 | pdb_00009h87

Crystal structure of LmrR variant V15aY with Val15 replaced by 3-aminotyrosine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294The protein solution contained 16 mg/ml protein in 20 mM HEPES, 280 mM NaCl, pH 7.0. The reservoir solution contained 0.2 M KSCN, 0.1 M Bis-Tris propane, pH 6.5, 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8757.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.714α = 90
b = 70.714β = 90
c = 59.838γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2023-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.96546ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1561.261000.050.0530.016117.410.29471
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.211001.8541.9510.6030.70510.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.1542.84899347499.950.223570.221220.23350.268190.2791RANDOM75.912
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]
-1.21-0.6-1.213.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.536
r_long_range_B_refined12.821
r_long_range_B_other12.819
r_scangle_other9.14
r_dihedral_angle_2_deg8.619
r_mcangle_other7.791
r_mcangle_it7.781
r_scbond_it6.502
r_scbond_other6.497
r_dihedral_angle_1_deg6.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.536
r_long_range_B_refined12.821
r_long_range_B_other12.819
r_scangle_other9.14
r_dihedral_angle_2_deg8.619
r_mcangle_other7.791
r_mcangle_it7.781
r_scbond_it6.502
r_scbond_other6.497
r_dihedral_angle_1_deg6.294
r_mcbond_it5.796
r_mcbond_other5.76
r_angle_refined_deg1.985
r_angle_other_deg0.697
r_chiral_restr0.102
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms928
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing