X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 10.5
Temperature 298.0
Details urate oxidase 8.5mg/ml, sodium carbonate 10mM, 8-azaxanthin 0.2mg/ml, PEG 8000 7% , pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.19 α = 90
b = 96.03 β = 90
c = 105.21 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2002-12-10
Diffraction Radiation
Monochromator Protocol
SI 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LURE BEAMLINE DW32 0.964 LURE DW32

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
1.75 99 99.9 0.055 -- -- -- -- 41239 1.0 1.0 18.9
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)
1.75 1.81 99.8 0.346 -- -- -- 4076

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 1.75 14.77 -- 0.0 -- 39086 2074 99.94 -- 0.16642 0.16528 0.18779 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 1.75 1.795 2944 145 2799 0.214 0.22 -- 99.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.03
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.124
r_angle_refined_deg 1.476
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.954
r_chiral_restr 0.104
r_nbd_refined 0.202
r_symmetry_vdw_refined 0.207
r_dihedral_angle_3_deg 13.338
r_mcbond_it 0.976
r_bond_refined_d 0.012
r_scbond_it 2.555
r_scangle_it 4.239
r_dihedral_angle_2_deg 37.143
r_symmetry_hbond_refined 0.148
r_dihedral_angle_4_deg 8.033
r_nbtor_refined 0.311
r_mcangle_it 1.678
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2362
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 198

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: 345DTB