X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch
pH 8.5
Temperature 298.0
Details 10-15 mg/ml urate oxidase, 2 mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.38 α = 90
b = 96.26 β = 90
c = 105.55 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r Mirrors 2008-07-11
Diffraction Radiation
Monochromator Protocol
Si 111 Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM16 0.979 ESRF BM16

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.62 30 98.5 -- 0.042 -- 4.9 -- 51415 -- 1.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.62 1.68 98.8 -- 0.414 3.8 5.0 5101

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
RIGID BODY 1.621 14.99 -- -- -- 48742 2624 98.59 -- 0.17435 0.17329 0.19388 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.621 1.663 -- 189 3520 0.236 0.244 -- 98.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.556
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.012
r_gen_planes_refined 0.007
r_chiral_restr 0.097
r_mcangle_it 1.703
r_dihedral_angle_1_deg 5.946
r_scbond_it 2.495
r_dihedral_angle_2_deg 38.692
r_dihedral_angle_3_deg 12.185
r_mcbond_it 0.886
r_scangle_it 4.207
r_dihedral_angle_4_deg 10.4
r_angle_refined_deg 1.379
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2362
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 191

Software

Software
Software Name Purpose
HKL-2000 data collection
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling