3RXY

Crystal structure of NIF3 superfamily protein from Sphaerobacter thermophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62770.1 M sodium acetate, 3.5 M sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.957.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.77α = 90
b = 96.483β = 115.28
c = 128.47γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2010-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97903APS19-BM

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
125099.40.13213.133.4139620138727-327.02
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)
122.0399.50.6872.163.46951

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTdifferent crystal form of the same protein solved by SAD238.3713872213872213730.20930.20930.20910.2317thin resolution shells28.2
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]
-0.21972.65513.3683-3.1486
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.57
t_other_torsion2.7
t_angle_deg1.15
t_bond_d0.014
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_chiral_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.57
t_other_torsion2.7
t_angle_deg1.15
t_bond_d0.014
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12382
Nucleic Acid Atoms
Solvent Atoms691
Heterogen Atoms53

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
BUSTERrefinement
HKL-3000data reduction
HKL-3000data scaling