4F8B

Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BP1PDB ENTRY 3BP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4293.1516-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride or magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.5251.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.507α = 90
b = 93.507β = 90
c = 193.696γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315rmirrors2006-04-10MSINGLE 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
12.50241.5698.70.1027.89.934623346231154.7
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)
12.5022.5789.90.292.16.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BP12.50241.563389732475172098.720.193340.189180.27195RANDOM42.536
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]
1.930.961.93-2.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.639
r_dihedral_angle_3_deg19.63
r_dihedral_angle_4_deg19.121
r_dihedral_angle_1_deg7.533
r_scangle_it4.348
r_scbond_it2.923
r_mcangle_it2.21
r_angle_refined_deg2.057
r_mcbond_it1.339
r_nbtor_refined0.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.639
r_dihedral_angle_3_deg19.63
r_dihedral_angle_4_deg19.121
r_dihedral_angle_1_deg7.533
r_scangle_it4.348
r_scbond_it2.923
r_mcangle_it2.21
r_angle_refined_deg2.057
r_mcbond_it1.339
r_nbtor_refined0.329
r_symmetry_vdw_refined0.254
r_nbd_refined0.251
r_metal_ion_refined0.238
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.177
r_chiral_restr0.129
r_bond_refined_d0.024
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6013
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms85

Software

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