3BJ6

Crystal structure of MarR family transcription regulator SP03579


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827715 % Ethanol, 0.1 M Imidazole pH 8.0, 0.2M MgCl2 pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8657.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.701α = 90
b = 55.778β = 90
c = 125.765γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3Mirrors2007-11-21MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9793, 0.9795APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1233.499.90.077.46.7269442694421.28
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.071000.2335.56.22644

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.0133.42552025520135399.890.1630.1630.16120.198RANDOM24.037
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]
0.10.3-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.553
r_dihedral_angle_4_deg22.259
r_dihedral_angle_3_deg14.928
r_dihedral_angle_1_deg4.548
r_scangle_it4.303
r_scbond_it2.855
r_mcangle_it1.482
r_angle_refined_deg1.381
r_mcbond_it1.316
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.553
r_dihedral_angle_4_deg22.259
r_dihedral_angle_3_deg14.928
r_dihedral_angle_1_deg4.548
r_scangle_it4.303
r_scbond_it2.855
r_mcangle_it1.482
r_angle_refined_deg1.381
r_mcbond_it1.316
r_nbtor_refined0.297
r_symmetry_vdw_refined0.273
r_nbd_refined0.217
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.147
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2370
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEphasing
ARP/wARPmodel building