X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IBAPDB ENTRY 2IBA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82984MG/ML URATE OXIDASE, 8-AZAXANTHINE 0.2MG/ML, TRIS 50MM, PEG 8000 2-5%, NACL 100MM, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
3.0159.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.502α = 90
b = 96.583β = 90
c = 106.005γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMAR scanner 345 mm plateMIRRORS2003-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLURE BEAMLINE DW320.964LUREDW32

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
11.752082.50.04934588116.39
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)
11.751.8144.30.0491813

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONrigid bodyTHROUGHOUTPDB ENTRY 2IBA1.7814.84133398167783.850.1660.1640.201RANDOM20.84
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.309
r_dihedral_angle_3_deg13.609
r_dihedral_angle_4_deg12.77
r_dihedral_angle_1_deg6.084
r_scangle_it4.079
r_scbond_it2.533
r_mcangle_it1.607
r_angle_refined_deg1.501
r_mcbond_it0.846
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.309
r_dihedral_angle_3_deg13.609
r_dihedral_angle_4_deg12.77
r_dihedral_angle_1_deg6.084
r_scangle_it4.079
r_scbond_it2.533
r_mcangle_it1.607
r_angle_refined_deg1.501
r_mcbond_it0.846
r_nbtor_refined0.304
r_nbd_refined0.198
r_symmetry_vdw_refined0.195
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.116
r_chiral_restr0.104
r_metal_ion_refined0.077
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection