1NF8

Crystal structure of PhzD protein active site mutant with substrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNative structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729810-20% polyethylene glycol 4000, 0.2M ammonium formate, 0.2% beta-octylglucoside, 1mM isochorismate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0247.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.4α = 90
b = 77.01β = 90
c = 82.44γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++OSMIC2002-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.62099.70.04222327572
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)
11.61.7990.2073.133895

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 REPLACEMENTFREE RNative structure1.6202740327403142392.90.1340.1340.1340.21RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
16081962
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.08
s_similar_adp_cmpnt0.055
s_non_zero_chiral_vol0.049
s_zero_chiral_vol0.047
s_from_restr_planes0.0279
s_angle_d0.026
s_anti_bump_dis_restr0.021
s_bond_d0.008
s_rigid_bond_adp_cmpnt0.003
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1629
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms36

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
d*TREKdata scaling
SHELXphasing