4FGC

Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4F8BPDB ENTRY 4F8B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.4293.1516-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride, VAPOR DIFFUSION, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.550.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.048α = 90
b = 93.048β = 90
c = 193.651γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315rmirrors2011-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-11.000003SSRLBL9-1

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
12.49822.15191.60.146.84344983157746.6
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)
12.4982.5488.80.652.33.91498

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 4F8B2.49822.153439729866159291.460.232250.228360.30485RANDOM39.309
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]
0.360.180.36-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.833
r_dihedral_angle_4_deg11.448
r_dihedral_angle_3_deg11.073
r_scangle_it3.033
r_dihedral_angle_1_deg2.322
r_angle_refined_deg1.997
r_scbond_it1.856
r_mcangle_it1.424
r_mcbond_it0.744
r_chiral_restr0.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.833
r_dihedral_angle_4_deg11.448
r_dihedral_angle_3_deg11.073
r_scangle_it3.033
r_dihedral_angle_1_deg2.322
r_angle_refined_deg1.997
r_scbond_it1.856
r_mcangle_it1.424
r_mcbond_it0.744
r_chiral_restr0.046
r_bond_refined_d0.016
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6007
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms84

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing