X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 294.0
Details sodium chloride, HEPES, ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.31 α = 90
b = 64.31 β = 90
c = 247.93 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
2 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV micro capillary focussing optic 1999-08-25
IMAGE PLATE RIGAKU RAXIS IV micro capillary focussing optic 1999-10-04
Diffraction Radiation
Monochromator Protocol
micro capillary focussing optic SINGLE WAVELENGTH
micro capillary focussing optic SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.5 20 90.0 0.072 -- -- 5.3 19293 17303 2.0 1.0 14.2
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)
2.5 2.59 72.0 0.439 -- 1.5 2.4 1347

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 2.6 20.0 2.0 2.0 19145 15856 1251 82.8 0.246 0.243 0.213 0.3 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 2.49 2.58 1106 74 1032 0.452 0.446 0.052 59.0
X Ray Diffraction 2.58 2.68 1291 109 1182 0.382 0.377 0.036 69.2
X Ray Diffraction 2.68 2.8 1510 153 1357 0.329 0.328 0.026 80.9
X Ray Diffraction 2.8 2.95 1643 145 1498 0.308 0.307 0.026 87.8
X Ray Diffraction 2.95 3.14 1689 116 1573 0.287 0.292 0.027 89.7
X Ray Diffraction 3.14 3.38 1663 125 1538 0.292 0.298 0.027 87.2
X Ray Diffraction 3.38 3.71 1621 121 1500 0.254 0.264 0.024 85.8
X Ray Diffraction 3.71 4.25 1598 122 1476 0.228 0.239 0.022 82.6
X Ray Diffraction 4.25 5.33 1703 125 1578 0.178 0.183 0.016 86.2
X Ray Diffraction 5.33 19.89 2032 161 1871 0.26 0.258 0.02 97.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 42.58
Anisotropic B[1][1] -2.836
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.836
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.672
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.8
x_torsion_deg 27.1
x_torsion_impr_deg 1.26
x_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.56
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3636
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 71

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement