4QMA

Crystal Structure of a Putative Cysteine Dioxygnase From Ralstonia eutropha: An Alternative Modeling of 2GM6 from JCSG Target 361076


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GM6Fourier Synthesis based on 2GM6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82772.4M (NH4)2SO4, 0.1M TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5565.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.007α = 90
b = 57.007β = 90
c = 216.683γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2006-03-13MMAD
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.00000SSRLBL9-2
2SYNCHROTRONSSRL BEAMLINE BL9-20.97925, 0.91837, 0.97882SSRLBL9-2

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
11.65451000.1130.02514.1214437744377
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)
11.651.681000.53351.3020.616.52185

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFourier Synthesis based on 2GM61.6544.7480.18200242041221799.870.17540.17410.2Same as ReCDO, random 5% to 1.65 Ang
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.641
f_angle_d1.213
f_chiral_restr0.052
f_bond_d0.014
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1499
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms49

Software

Software
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing