3E97

Crystal structure of transcriptional regulator of Crp/Fnr family (YP_604437.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 1.86 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.82770.2000M KAcetate, 20.0000% PEG-3350, No Buffer pH 7.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.4950.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68α = 90
b = 68β = 90
c = 111.45γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-08-06MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97929SSRLBL11-1

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
11.8629.39999.80.06717.8411.4522704-326.147
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)
1.861.9399.60.6312.43

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 DIFFRACTIONMADTHROUGHOUT1.8629.39922645115899.870.210.2080.246RANDOM30.37
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]
-0.77-0.771.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.754
r_dihedral_angle_4_deg11.77
r_dihedral_angle_3_deg10.499
r_scangle_it6.283
r_scbond_it4.467
r_dihedral_angle_1_deg3.067
r_mcangle_it2.96
r_mcbond_it2.034
r_angle_refined_deg1.458
r_angle_other_deg0.953
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.754
r_dihedral_angle_4_deg11.77
r_dihedral_angle_3_deg10.499
r_scangle_it6.283
r_scbond_it4.467
r_dihedral_angle_1_deg3.067
r_mcangle_it2.96
r_mcbond_it2.034
r_angle_refined_deg1.458
r_angle_other_deg0.953
r_mcbond_other0.458
r_symmetry_vdw_other0.292
r_nbd_refined0.214
r_nbd_other0.201
r_symmetry_vdw_refined0.176
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.119
r_chiral_restr0.086
r_nbtor_other0.083
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1762
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction