1O4T | pdb_00001o4t

Crystal structure of a predicted oxalate decarboxylase (tm1287) from thermotoga maritima at 1.95 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FI2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1629320 % PEG 6000, 1.0 M LiCl, 0.1 M MES, pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.00
Crystal Properties
Matthews coefficientSolvent content
2.5551.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.132α = 90
b = 49.738β = 123.73
c = 69.547γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315FLAT MIRROR2002-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9525.2995.40.08310.43.51775836.93
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.06880.5551.82.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FI21.9525.291687588395.20.1630.160.170.2170.23RANDOM32.48
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]
1.91.66-0.05-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.595
r_dihedral_angle_3_deg14.126
r_dihedral_angle_4_deg11.733
r_dihedral_angle_1_deg6.172
r_scangle_it4.474
r_scbond_it2.675
r_angle_refined_deg1.568
r_mcangle_it1.483
r_angle_other_deg0.849
r_mcbond_it0.802
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1772
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms14

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling