X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3
Temperature 295.0
Details PEG 4000, ammonium sulfate, nikkel sulfate, sodium citrate, pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.01 α = 114.32
b = 84.13 β = 98
c = 96.04 γ = 89.75
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 diamond crystal, Ge crystal and toroidal mirror 2001-11-29
Diffraction Radiation
Monochromator Protocol
diamond crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.934 ESRF ID14-2

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
1.7 37 97.5 0.043 0.043 -- 2.1 210531 205268 0.0 0.0 21.0
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)
1.7 1.74 95.6 0.384 0.384 2.1 1.7 --

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 1.7 35.81 0.0 0.0 195322 195322 10409 97.5 0.176 0.176 0.175 0.209 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 1.7 1.744 14607 338 -- 0.269 0.31 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 25.0
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] -0.01
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.751
r_bond_other_d 0.941
r_bond_refined_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14664
Nucleic Acid Atoms 0
Heterogen Atoms 412
Solvent Atoms 1353

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
EPMR Structure Solution
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
EPMR model building
TRUNCATE data reduction
DENZO data collection