4IQL

Crystal Structure of Porphyromonas gingivalis Enoyl-ACP Reductase II (FabK) with cofactors NADPH and FMN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z6JPDB ENTRY 2Z6J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729120% PEG 3350, 0.2M sodium formate, 5mM MOPS (pH 7.0), 1mM DTT. 3uL(protein stock):3uL(Index 90):1uL Seed stock. (Seed Stock From: 10% PEG 3350, 0.15M Na Citrate pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2545.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.652α = 90
b = 86.652β = 90
c = 150.505γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252012-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

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
11.9382099.50.1340.13415.27.190851908511120.56
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)
11.9382.0597.50.5384.196.814235

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Z6J1.938204795145527242499.710.163310.163310.1610.20695RANDOM13.324
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]
-0.190.4-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.272
r_dihedral_angle_4_deg18.473
r_dihedral_angle_3_deg13.33
r_dihedral_angle_1_deg12.864
r_scangle_it6.401
r_scbond_it3.96
r_mcangle_it2.166
r_angle_refined_deg1.606
r_mcbond_it1.279
r_chiral_restr0.123
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.272
r_dihedral_angle_4_deg18.473
r_dihedral_angle_3_deg13.33
r_dihedral_angle_1_deg12.864
r_scangle_it6.401
r_scbond_it3.96
r_mcangle_it2.166
r_angle_refined_deg1.606
r_mcbond_it1.279
r_chiral_restr0.123
r_bond_refined_d0.017
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4638
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms190

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling