X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 50 mM Sodium Cacodylate, 50-125 mM Sodium Citrate, 10-20 % isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.22 α = 90
b = 70.22 β = 90
c = 119.23 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Varimax-HR 2009-04-10
Diffraction Radiation
Monochromator Protocol
Varimax-HR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5416 -- --

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
2.7 50 98.2 0.058 -- -- 10.2 -- 5938 -- -- --
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)
2.7 2.8 87.5 0.201 -- -- 5.6 525

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 2.7 29.462 -- 1.0 -- 5394 313 89.3 -- 0.237 0.236 0.252 --
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 2.7 2.8 -- 161 2395 0.242 0.297 -- 85.0
X Ray Diffraction 3.397 29.463 -- 152 2686 0.234 0.237 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 95.717
Anisotropic B[1][1] -30.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -30.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 60.739
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_angle_d 0.803
f_plane_restr 0.003
f_dihedral_angle_d 13.781
f_chiral_restr 0.043
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1294
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 12

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.005
StructureStudio data collection
PHASER phasing