5H1A

Crystal structure of an IclR homolog from Microbacterium sp. strain HM58-2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION82931M (NH4)2HPO4
Crystal Properties
Matthews coefficientSolvent content
2.5150.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.889α = 90
b = 155.375β = 90
c = 83.262γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS3 S 6M2015-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.038Photon FactoryBL-17A

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
12.15098.924.96.769549
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.14

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 DIFFRACTIONSADTHROUGHOUT2.143.666018348998.440.227630.226880.24187RANDOM39.174
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]
1.220.37-1.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.725
r_dihedral_angle_4_deg18.782
r_dihedral_angle_3_deg15.474
r_dihedral_angle_1_deg5.746
r_long_range_B_refined4.929
r_long_range_B_other4.929
r_angle_other_deg3.675
r_scangle_other3.314
r_mcangle_it2.773
r_mcangle_other2.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.725
r_dihedral_angle_4_deg18.782
r_dihedral_angle_3_deg15.474
r_dihedral_angle_1_deg5.746
r_long_range_B_refined4.929
r_long_range_B_other4.929
r_angle_other_deg3.675
r_scangle_other3.314
r_mcangle_it2.773
r_mcangle_other2.773
r_scbond_it1.973
r_scbond_other1.969
r_mcbond_it1.668
r_mcbond_other1.667
r_angle_refined_deg1.462
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d
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 Atoms7342
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing