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_bond_d 0.009
c_angle_deg 1.56
c_dihedral_angle_d 25.08
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

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