X-RAY DIFFRACTION Experimental Data & Validation


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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_improper_angle_d 0.81
c_dihedral_angle_d 25.6
c_angle_deg 1.3
c_bond_d 0.007
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
SOLVE model building
SCALEPACK data reduction
DENZO data collection