X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Chill Tube Containing Protein to 265 K Then Bring to 295 K
pH 7
Temperature 295.0
Details 100 mM Phosphate, 20 mM DTT, pH 7.0, chill tube containing protein to 265 K, then bring to 295 K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.85 α = 90
b = 57.85 β = 90
c = 98.71 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 296
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II MIRRORS 1999-06-26
Diffraction Radiation
Monochromator Protocol
Ni Filter SINGLE WAVELENGTH
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
2.4 20 97.1 0.074 0.074 -- 10.0 -- 6843 -- 2.0 28.0
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)
2.4 2.44 92.8 0.146 0.146 9.6 7.5 6843

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 2.4 20.0 2.0 2.0 -- 6667 679 95.3 -- -- 0.223 0.243 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 2.4 2.55 -- 112 924 0.242 0.273 0.023 92.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 13.2
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
x_bond_d 0.012
x_dihedral_angle_d 28.6
x_angle_deg 1.3
x_improper_angle_d 6.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.23
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1458
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 71

Software

Software
Software Name Purpose
AMoRE phasing
X-PLOR refinement version: 3.843
DENZO data reduction
SCALEPACK data scaling