3HNH

Crystal Structure of PqqC Active Site Mutant Y175S,R179S in complex with a reaction intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OTVPDB ENTRY 1OTV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.2M Sodium chloride, 0.1M Tris pH 8.5, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.792α = 90
b = 115.347β = 90
c = 67.062γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.849.62997.70.0740.06613.74.526201
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.995.40.6880.5851.83.63686

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1OTV1.849.62926199131597.320.190.1890.22RANDOM44.854
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]
0.44-0.790.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.786
r_dihedral_angle_3_deg15.531
r_dihedral_angle_4_deg13.573
r_dihedral_angle_1_deg4.915
r_scangle_it3.553
r_scbond_it2.43
r_angle_refined_deg1.573
r_mcangle_it1.561
r_mcbond_it1.125
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.786
r_dihedral_angle_3_deg15.531
r_dihedral_angle_4_deg13.573
r_dihedral_angle_1_deg4.915
r_scangle_it3.553
r_scbond_it2.43
r_angle_refined_deg1.573
r_mcangle_it1.561
r_mcbond_it1.125
r_nbtor_refined0.309
r_nbd_refined0.219
r_symmetry_vdw_refined0.185
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.151
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1927
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms24

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction