X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Details CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION. THE HANGING DROPS CONSISTED OF 2UL OF PROTEIN SOLUTION CONTAINING EACH PROTEIN AT 1MG/ML IN 0.1 % SODIUM AZIDE, 20MM TRIS-HCL AT PH 7.0, MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION TO BE SCREENED. CRYSTALS WERE OBTAINED WITH RESERVOIR SOLUTIONS CONTAINING 17.5 - 22.5 % (W/V) POLYETHYLENE GLYCOL (MEAN MW 8000) IN 0.1 % SODIUM AZIDE, 100MM TRIS-HCL, PH 7.0, AT TEMPERATURES BETWEEN 17.5 AND 21.5 (CELSIUS)., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.35 α = 90
b = 81.95 β = 98.27
c = 64.24 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 278
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II COLLIMATOR 1994-06
Diffraction Radiation
Monochromator Protocol
GRAPHITE --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
3.15 15 98.3 0.113 -- -- 3.1 -- 14109 -- 3.0 25.4
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)
3.15 3.31 98.8 0.265 -- 2.8 3.1 --

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 3.15 8.0 -- 0.0 -- 11603 756 86.0 -- 0.225 0.225 0.289 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 3.15 3.26 -- 53 902 0.288 0.367 0.05 70.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUPED B-FACTOR REFINEMENT
Mean Isotropic B 33.1
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.06
x_bond_d 0.005
x_angle_deg 1.18
x_dihedral_angle_d 26.47
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.52
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4977
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
AMORE model building
CCP4 data reduction
DENZO data collection