3ITY

Metal-free form of Pseudomonas stutzeri L-rhamnose isomerase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HCVPDB ENTRY 2HCV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32987-8% (W/V) polyethylene glycol 20000, 50mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2144.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.691α = 90
b = 104.785β = 107.98
c = 114.252γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2006-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A0.978Photon FactoryBL-6A

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
11.845099.80.061113.714524414524412.4
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)
1.841.9199.20.2755.23.6

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 2HCV1.8446.9414056114056114044970.160.1580.1580.19RANDOM16
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]
-0.96-1.54-0.181.14
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.3
c_angle_deg1.1
c_improper_angle_d0.74
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13072
Nucleic Acid Atoms
Solvent Atoms1985
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling