3BOS

Crystal structure of a putative dna replication regulator HDA (SAMA_1916) from Shewanella amazonensis sb2b at 1.75 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9277NANODROP, 0.2M Sodium thiocyanate, 20% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4750.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.037α = 90
b = 64.032β = 90
c = 153.64γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2007-11-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97932, 0.91837SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7529.55399.70.1020.1025.23.75543619.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.81000.6430.6431.23.74067

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 DIFFRACTIONMADTHROUGHOUT1.7529.55355402281399.540.1680.1660.201RANDOM16.815
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]
-0.120.74-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.638
r_dihedral_angle_4_deg15.132
r_dihedral_angle_3_deg12.442
r_scangle_it6.212
r_dihedral_angle_1_deg4.491
r_scbond_it4.456
r_mcangle_it2.551
r_mcbond_it1.585
r_angle_refined_deg1.474
r_angle_other_deg0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.638
r_dihedral_angle_4_deg15.132
r_dihedral_angle_3_deg12.442
r_scangle_it6.212
r_dihedral_angle_1_deg4.491
r_scbond_it4.456
r_mcangle_it2.551
r_mcbond_it1.585
r_angle_refined_deg1.474
r_angle_other_deg0.98
r_mcbond_other0.72
r_symmetry_vdw_refined0.494
r_symmetry_vdw_other0.351
r_nbd_refined0.231
r_nbd_other0.201
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.175
r_symmetry_hbond_refined0.146
r_metal_ion_refined0.117
r_chiral_restr0.087
r_nbtor_other0.086
r_bond_refined_d0.014
r_xyhbond_nbd_other0.006
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3574
Nucleic Acid Atoms
Solvent Atoms554
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing