1AL8

THREE-DIMENSIONAL STRUCTURE OF GLYCOLATE OXIDASE WITH BOUND ACTIVE-SITE INHIBITORS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GOXPDB ENTRY 1GOX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.3PROTEIN WAS CRYSTALLIZED FROM 50MM TRIS- BUFFER, 0.25 MG/ML FMN, 4% TERTIARY BUTANOL AND 0.5 % JF 5969, PH 8.3. JF 5969 IS A MIXTURE OF SYMPERONIC NPE1800 (33.3G/L), TWEEN 85 (20G/L) IN CYCLOHEXANONE.
Crystal Properties
Matthews coefficientSolvent content
2.554.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.4α = 90
b = 95.4β = 90
c = 93.5γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMARRESEARCH1996-04-06M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
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
12.210099.80.0947.911.1213080.317
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)
12.22.2599.90.3693.3

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GOX2.282119816611000.1940.1940.251RANDOM0.276
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
x_dihedral_angle_d23.78
x_angle_deg1.37
x_improper_angle_d1.246
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.78
x_angle_deg1.37
x_improper_angle_d1.246
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2649
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms49

Software

Software
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling