X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 3.5~4M Sodium Formate, 50mM Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 188.76 α = 90
b = 188.76 β = 90
c = 188.76 γ = 90
Symmetry
Space Group P 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-11-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 1.0069 APS 14-ID-B

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
2.54 84.42 99.4 0.09 -- -- 33.0 70833 70394 0.0 -- 53.5
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)
2.55 2.64 100.0 0.33 -- 20.0 -- 3710

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
-- 2.55 84.42 -- -- 70831 70394 2805 99.4 -- -- 0.269 0.309 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 2.55 2.67 8623 305 8318 0.422 0.411 0.024 97.3
X Ray Diffraction 2.67 2.81 8755 355 8400 0.355 0.349 0.019 98.9
X Ray Diffraction 2.81 2.98 8822 333 8489 0.316 0.316 0.017 99.5
X Ray Diffraction 2.98 3.21 8805 392 8413 0.287 0.292 0.015 99.5
X Ray Diffraction 3.21 3.54 8869 342 8527 0.278 0.284 0.015 99.9
X Ray Diffraction 3.54 4.05 8824 361 8463 0.23 0.235 0.012 99.6
X Ray Diffraction 4.05 5.1 8877 366 8511 0.206 0.208 0.011 100.0
X Ray Diffraction 5.1 84.42 8819 351 8468 0.259 0.258 0.014 99.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.79
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
c_angle_deg 1.3
c_dihedral_angle_d 25.6
c_bond_d 0.007
c_improper_angle_d 0.81
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.52
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.56
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6464
Nucleic Acid Atoms 0
Heterogen Atoms 442
Solvent Atoms 50

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
CNS refinement version: 1.0