X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 2.5
Temperature 293.0
Details ammonium sulphate, glycin/HCl, lactose, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.28 α = 90
b = 106.28 β = 90
c = 312.33 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2000-04-28
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9073 EMBL/DESY, HAMBURG X11

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
2.3 25.97 99.6 0.036 0.049 -- 7.0 -- 47510 0.0 1.0 38.9
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)
2.3 2.34 99.3 0.368 0.322 3.93 6.4 47288

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 10.0 3.0 3.0 46667 46562 2320 99.8 0.2501 0.2413 0.207 0.232 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 5677 279 5398 0.302 0.306 0.018 99.3
X Ray Diffraction 2.4 2.53 5713 273 5440 0.258 0.261 0.016 99.5
X Ray Diffraction 2.53 2.68 5719 282 5437 0.239 0.242 0.014 99.7
X Ray Diffraction 2.68 2.89 5763 314 5449 0.207 0.208 0.012 99.7
X Ray Diffraction 2.89 3.17 5792 288 5504 0.21 0.209 0.012 99.6
X Ray Diffraction 3.17 3.61 5834 305 5529 0.194 0.192 0.011 99.8
X Ray Diffraction 3.61 4.48 5918 298 5620 0.168 0.166 0.01 99.9
X Ray Diffraction 4.48 10.0 6146 281 5865 0.213 0.215 0.013 99.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 39.16
Anisotropic B[1][1] 3.55
Anisotropic B[1][2] 5.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.09
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.965
c_dihedral_angle_d 25.08
c_angle_deg 1.56
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3921
Nucleic Acid Atoms 0
Heterogen Atoms 260
Solvent Atoms 328

Software

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