X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microdialysis
pH 8
Temperature 298.0
Details concentrated solution of the protein (50-80 mg mL-1), 0.01 M Tris-HCl, pH 8.0, 12% (v/v) isopropanol, MICRODIALYSIS, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 151.3 α = 90
b = 151.3 β = 90
c = 48.6 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC graphite monochromator 1994-03-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200B 1.5418 -- --

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
3 50 96.0 0.115 -- -- 2.8 -- 23431 4.0 -- --
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)
3.0 3.11 93.0 0.418 0.418 1.8 2.4 --

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
MOLECULAR REPLACEMENT 3.0 10.0 2.0 4.0 23431 21955 795 93.9 0.1413 -- 0.139 0.199 RANDOM, PLUS TWIN-RELATED MATES
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 3.0 3.11 2267 74 -- 0.239 0.287 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model INDIVIDUAL, WITH TIGHT ADJACENCY AND NCS RESTRAINTS, AND IDENTITY CONSTRAINTS ON NEARLY CHEMICALLY EQUIVALENT REDIDUES (E.G. OE1 AND OE2 OF GLU)
Mean Isotropic B 31.1
RMS Deviations
Key Refinement Restraint Deviation
s_anti_bump_dis_restr 0.017
s_rigid_bond_adp_cmpnt 0.0
s_non_zero_chiral_vol 0.03
s_similar_dist 0.012
s_similar_adp_cmpnt 0.026
s_approx_iso_adps 0.0
s_angle_d 0.017
s_zero_chiral_vol 0.023
s_bond_d 0.005
s_from_restr_planes 0.177
Coordinate Error
Parameter Value
Number Disordered Residues 0.0
Occupancy Sum Hydrogen 0.0
Occupancy Sum Non Hydrogen 5241.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5114
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 127

Software

Software
Software Name Purpose
DENZO data reduction
ROTAVATA-AGROVATA data reduction
X-PLOR/BRUTE model building
SHELXL-97 refinement
CCP4 data scaling version: (AGROVATA
ROTAVATA) data scaling
X-PLOR phasing
BRUTE phasing