3HLX

Crystal Structure of PqqC Active Site Mutant Y175F in Complex with PQQ


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350, vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3848.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.607α = 90
b = 116.775β = 90
c = 68.279γ = 90
Symmetry
Space GroupP 21 21 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
11.337.788.40.1880.17310.56.5124411
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)
1.31.3753.10.8550.7381.3310702

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 1OTV1.337.7124354623288.240.1650.1640.198RANDOM12.088
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]
-0.63-0.711.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.688
r_dihedral_angle_4_deg16.447
r_dihedral_angle_3_deg13.102
r_sphericity_free9.607
r_dihedral_angle_1_deg5.758
r_scangle_it4.361
r_sphericity_bonded4.155
r_scbond_it3.358
r_mcangle_it2.376
r_mcbond_it1.897
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.688
r_dihedral_angle_4_deg16.447
r_dihedral_angle_3_deg13.102
r_sphericity_free9.607
r_dihedral_angle_1_deg5.758
r_scangle_it4.361
r_sphericity_bonded4.155
r_scbond_it3.358
r_mcangle_it2.376
r_mcbond_it1.897
r_angle_refined_deg1.708
r_rigid_bond_restr1.643
r_angle_other_deg1.162
r_mcbond_other0.824
r_symmetry_vdw_refined0.603
r_symmetry_hbond_refined0.494
r_symmetry_vdw_other0.488
r_nbd_refined0.242
r_nbd_other0.211
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.161
r_chiral_restr0.11
r_nbtor_other0.083
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4152
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms74

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction