X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.2
Temperature 298.0
Details Protein Solution (11.4 mg/ml SsfS6 protein, 50mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.13~1.26 M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 8.2) Cryoprotected with 100% Paratone-N, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.14 α = 90
b = 81.14 β = 90
c = 229.91 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-06-10
Diffraction Radiation
Monochromator Protocol
Kohzu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.12715 APS 21-ID-D

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
2.4 50 99.5 0.2 -- -- 15.9 18241 18150 0.0 0.0 --
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)
2.4 2.44 100.0 -- -- -- 14.2 887

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 2.405 44.49 -- 1.36 18271 18057 897 98.83 -- 0.2454 0.2441 0.2692 RANDOM, ASSIGN TEST SET IN THIN RESOLUTION SHELLS
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 2.4054 2.556 -- 132 2723 0.3249 0.3872 -- 96.0
X Ray Diffraction 2.556 2.7534 -- 165 2774 0.2903 0.3364 -- 100.0
X Ray Diffraction 2.7534 3.0304 -- 125 2855 0.2758 0.2826 -- 100.0
X Ray Diffraction 3.0304 3.4688 -- 147 2859 0.2494 0.3033 -- 100.0
X Ray Diffraction 3.4688 4.3697 -- 165 2894 0.2201 0.2577 -- 100.0
X Ray Diffraction 4.3697 44.4973 -- 163 3055 0.2355 0.2432 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.2766
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.8
f_angle_d 0.758
f_chiral_restr 0.049
f_bond_d 0.003
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2679
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 67

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8_1063
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
HKL-2000 data reduction
PHENIX phasing version: PHASER