3W5I

Crystal structure of NfeoB from Gallionella capsiferriformans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IBYPDB ENTRY 3IBY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82891M Ammonium sulphate, 0.1M Bis-Tris pH 5.5, 1% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.0559.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.683α = 90
b = 112.533β = 90
c = 97.866γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1575.03599.50.08314.87303863038636.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2799.20.7170.7170.7720.2841.17.24371

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3IBY2.1575.033036730367148099.210.22380.22380.22190.2616RANDOM37.4447
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]
-1.11.070.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.532
r_dihedral_angle_4_deg17.544
r_dihedral_angle_3_deg13.786
r_dihedral_angle_1_deg5.461
r_scangle_it2.766
r_scbond_it1.65
r_mcangle_it1.18
r_angle_refined_deg1.097
r_angle_other_deg0.822
r_mcbond_it0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.532
r_dihedral_angle_4_deg17.544
r_dihedral_angle_3_deg13.786
r_dihedral_angle_1_deg5.461
r_scangle_it2.766
r_scbond_it1.65
r_mcangle_it1.18
r_angle_refined_deg1.097
r_angle_other_deg0.822
r_mcbond_it0.62
r_mcbond_other0.094
r_chiral_restr0.062
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3016
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms15

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction