2NVM

Crystal structure of fdxN element excision controlling factor XisI (YP_321976.1) from Anabaena Variabilis ATCC 29413 at 2.19 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP627730.0% PEG-6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8656.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.44α = 90
b = 122.44β = 90
c = 77.076γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-13MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000, 0.9795, 0.9792ALS8.2.2

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
12.162.381000.1070.10712.410.41806449.03
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)
12.192.311001.3751.3751.810.72564

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 DIFFRACTIONMADTHROUGHOUT2.1977.1521801591799.880.2030.2010.244RANDOM45.913
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]
0.510.250.51-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.127
r_dihedral_angle_4_deg10.615
r_dihedral_angle_3_deg10.47
r_scangle_it5.85
r_scbond_it4.351
r_dihedral_angle_1_deg3.223
r_mcangle_it2.64
r_mcbond_it1.94
r_angle_refined_deg1.895
r_angle_other_deg1.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.127
r_dihedral_angle_4_deg10.615
r_dihedral_angle_3_deg10.47
r_scangle_it5.85
r_scbond_it4.351
r_dihedral_angle_1_deg3.223
r_mcangle_it2.64
r_mcbond_it1.94
r_angle_refined_deg1.895
r_angle_other_deg1.614
r_mcbond_other0.356
r_nbd_refined0.15
r_nbtor_refined0.137
r_symmetry_vdw_other0.134
r_nbd_other0.131
r_symmetry_vdw_refined0.122
r_chiral_restr0.116
r_xyhbond_nbd_refined0.115
r_symmetry_hbond_refined0.077
r_nbtor_other0.066
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1754
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SHELXDphasing
autoSHARPphasing