3BJA

Crystal structure of putative MarR-like transcription regulator (NP_978771.1) from Bacillus cereus ATCC 10987 at 2.38 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277NANODROP, 24.9% PEG 3350, 0.214M Potassium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5251.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.321α = 90
b = 71.321β = 90
c = 65.72γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2007-10-25MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.94939, 0.97953, 0.97939APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.3848.33799.70.06116.257225-368.524
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)
12.382.461000.8792.2

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 DIFFRACTIONMADTHROUGHOUT2.3848.337719433799.760.2340.2330.253RANDOM64.8
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]
0.660.66-1.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.113
r_dihedral_angle_4_deg14.904
r_dihedral_angle_3_deg13.418
r_scangle_it7.107
r_scbond_it5.211
r_dihedral_angle_1_deg2.977
r_mcangle_it2.726
r_mcbond_it1.937
r_angle_refined_deg1.549
r_angle_other_deg1.262
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.113
r_dihedral_angle_4_deg14.904
r_dihedral_angle_3_deg13.418
r_scangle_it7.107
r_scbond_it5.211
r_dihedral_angle_1_deg2.977
r_mcangle_it2.726
r_mcbond_it1.937
r_angle_refined_deg1.549
r_angle_other_deg1.262
r_mcbond_other0.271
r_nbd_refined0.175
r_symmetry_hbond_refined0.16
r_nbtor_refined0.148
r_symmetry_vdw_other0.139
r_xyhbond_nbd_refined0.12
r_nbd_other0.119
r_symmetry_vdw_refined0.113
r_chiral_restr0.086
r_nbtor_other0.075
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1109
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing