X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details PEG 8000, sodium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.6 α = 90
b = 54.38 β = 90
c = 94.89 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC mirrors 1998-01-01
Diffraction Radiation
Monochromator Protocol
graphite 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
2.1 36.55 94.3 -- -- -- -- 12225 11792 0.0 2.0 9.1
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)
2.1 2.19 96.7 -- 0.345 -- 3.9 11787

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
MAD 2.1 36.55 2.0 0.0 12500 11792 1217 94.3 0.269 0.208 0.208 0.269 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 2.1 2.2 1396 135 1261 0.216 0.219 0.019 91.5
X Ray Diffraction 2.2 2.31 1418 139 1279 0.185 0.188 0.016 93.2
X Ray Diffraction 2.31 2.46 1459 152 1307 0.198 0.196 0.016 94.3
X Ray Diffraction 2.46 2.65 1474 157 1317 0.204 0.202 0.016 95.4
X Ray Diffraction 2.65 2.91 1467 139 1328 0.204 0.204 0.017 95.4
X Ray Diffraction 2.91 3.33 1532 168 1364 0.218 0.22 0.017 97.4
X Ray Diffraction 3.33 4.2 1528 173 1355 0.197 0.2 0.015 96.0
X Ray Diffraction 4.2 36.55 1518 154 1364 0.229 0.227 0.018 90.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.1
Anisotropic B[1][1] -2.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.43
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 0.64
x_torsion_deg 15.2
x_angle_deg 0.9
x_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.05
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1692
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 206

Software

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