X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 277.0
Details Magnesium Acetate, Sodium Cacodylate, MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.32 α = 90
b = 139.32 β = 90
c = 231.01 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC YALE MIRRORS 2000-10-24
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.2 99 95.5 0.046 -- -- 2.5 48993 55327 0.0 0.0 42.6
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)
2.2 2.28 83.1 0.433 -- 1.46 1.83 4729

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 2.3 19.9 0.0 0.0 50531 48993 2403 97.0 -- -- 0.179 0.204 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 2.3 2.4 5960 308 5652 0.291 0.327 0.019 95.7
X Ray Diffraction 2.4 2.53 6079 298 5781 0.252 0.301 0.017 97.2
X Ray Diffraction 2.53 2.69 6068 318 5750 0.215 0.259 0.015 97.5
X Ray Diffraction 2.69 2.9 6142 267 5875 0.197 0.238 0.015 97.8
X Ray Diffraction 2.9 3.19 6145 311 5834 0.191 0.221 0.013 97.8
X Ray Diffraction 3.19 3.65 6183 308 5875 0.185 0.19 0.011 97.7
X Ray Diffraction 3.65 4.58 6152 305 5847 0.148 0.175 0.01 96.5
X Ray Diffraction 4.58 19.9 6264 288 5976 0.151 0.165 0.01 94.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 44.58
Anisotropic B[1][1] 5.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.32
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.005
c_angle_deg 1.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3532
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 425

Software

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