X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 300.0
Details 50 mM Sodium Cacodylate, 50-125 mM Sodium Citrate, 10-20% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.56 α = 90
b = 70.56 β = 90
c = 118.33 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-HF 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
2.46 50 97.6 0.043 -- -- 5.5 -- 7821 -- -- --
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)
2.46 2.55 99.2 0.131 -- -- 5.3 781

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 2.46 22.667 -- 1.97 -- 7790 354 97.25 -- 0.211 0.21 0.246 --
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 2.46 2.55 -- 135 2513 0.251 0.312 -- 99.0
X Ray Diffraction 2.81 3.538 -- 111 2537 0.208 0.316 -- 99.0
X Ray Diffraction 3.538 22.668 -- 108 2386 0.197 0.205 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.239
Anisotropic B[1][1] -17.631
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -17.631
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 35.262
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_chiral_restr 0.043
f_plane_restr 0.003
f_angle_d 0.767
f_dihedral_angle_d 14.253
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1389
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 28

Software

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