7M1N | pdb_00007m1n

Wild-type Hydrogenobacter thermophilus ferredoxin 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IQZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28979% saturated ammonium sulfate, 0.1 M MES (pH 6.5)
Crystal Properties
Matthews coefficientSolvent content
2.0640.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.635α = 90
b = 69.103β = 90
c = 95.788γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.062898.90.982.26.61562117.0650310623
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.062.1388.90.762.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1IQZ2.06281.3474801790615605155798.40459074280.194659259040.1925542713280.20.2129546645640.2229.1412151389
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d10.0694193413
f_angle_d2.75845681966
f_chiral_restr0.0355841431777
f_bond_d0.0134412479267
f_plane_restr0.00353704188748
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms16

Software

Software
Software NamePurpose
PHENIXphasing
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling