3HML

Crystal Structure of PqqC Active Site Mutant H154S in Complex with PQQ


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OTWPDB ENTRY 1OTW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.0M Ammonium sulfate, 0.1M HEPES pH 7.0, 0.5% w/v Polyethylene glycol 8000, vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5251.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.06α = 90
b = 118.291β = 90
c = 68.04γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR555 FLAT PANEL2008-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8148EMBL/DESY, HAMBURGX11

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
12.3539.4499.70.1070.09913.66.725868
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)
2.352.4898.40.8120.7311.75.33640

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 1OTW2.3538.3725842131199.580.2150.2120.261RANDOM46.347
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]
-0.31-0.030.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg17.059
r_dihedral_angle_3_deg16.905
r_dihedral_angle_1_deg6.597
r_scangle_it3.071
r_scbond_it2.121
r_angle_refined_deg1.696
r_mcangle_it1.533
r_mcbond_it0.949
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg17.059
r_dihedral_angle_3_deg16.905
r_dihedral_angle_1_deg6.597
r_scangle_it3.071
r_scbond_it2.121
r_angle_refined_deg1.696
r_mcangle_it1.533
r_mcbond_it0.949
r_nbtor_refined0.3
r_nbd_refined0.21
r_symmetry_vdw_refined0.209
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.159
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3856
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms48

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction