7QAR

Serial crystallography structure of cofactor-free urate oxidase in complex with the 5-peroxo derivative of 9-methyl uric acid at room temperature


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CW2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7.6291TRIS-ACETATE, PEG 8000, MUA,
Crystal Properties
Matthews coefficientSolvent content
3.0159.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.79α = 90
b = 96.03β = 90
c = 105.21γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6M2019-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.03PETRA III, DESYP11

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.317.0799.980.8490.36682.4428.218280
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341000.2251.93690.5220.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4CW22.317.071828091999.640.2210.21820.266136.703
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]
1.332-0.446-0.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.473
r_dihedral_angle_3_deg14.087
r_dihedral_angle_4_deg13.027
r_dihedral_angle_1_deg6.931
r_lrange_it4.195
r_lrange_other4.194
r_mcangle_other2.81
r_mcangle_it2.809
r_scangle_it2.67
r_scangle_other2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.473
r_dihedral_angle_3_deg14.087
r_dihedral_angle_4_deg13.027
r_dihedral_angle_1_deg6.931
r_lrange_it4.195
r_lrange_other4.194
r_mcangle_other2.81
r_mcangle_it2.809
r_scangle_it2.67
r_scangle_other2.67
r_mcbond_it1.612
r_mcbond_other1.611
r_scbond_it1.522
r_scbond_other1.522
r_angle_other_deg1.438
r_angle_refined_deg1.388
r_nbd_other0.207
r_nbd_refined0.203
r_symmetry_nbd_other0.176
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.148
r_symmetry_xyhbond_nbd_refined0.125
r_symmetry_nbd_refined0.123
r_symmetry_nbtor_other0.079
r_chiral_restr0.071
r_ext_dist_refined_d0.009
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2359
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing