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 (1.13~1.40 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 = 82.61 α = 90
b = 82.61 β = 90
c = 230.52 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-06-02
CCD MARMOSAIC 300 mm CCD -- 2012-03-31
Diffraction Radiation
Monochromator Protocol
Kohzu SINGLE WAVELENGTH
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.12715 APS 21-ID-D
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G

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 99.0 0.094 -- -- 11.5 19209 19017 0.0 0.0 70.76
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 92.2 -- -- -- 10.1 858

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
SAD 2.397 30.763 -- 1.34 19126 18899 979 98.81 -- 0.226 0.2241 0.2617 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 2.3975 2.5238 -- 131 2411 0.3037 0.3414 -- 96.0
X Ray Diffraction 2.5238 2.6818 -- 173 2486 0.2794 0.3503 -- 100.0
X Ray Diffraction 2.6818 2.8888 -- 97 2577 0.2633 0.2722 -- 100.0
X Ray Diffraction 2.8888 3.1792 -- 147 2555 0.2417 0.3403 -- 100.0
X Ray Diffraction 3.1792 3.6386 -- 147 2561 0.2129 0.283 -- 100.0
X Ray Diffraction 3.6386 4.5818 -- 147 2624 0.1949 0.1994 -- 100.0
X Ray Diffraction 4.5818 30.7655 -- 137 2706 0.2274 0.2627 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.7201
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.044
f_bond_d 0.004
f_angle_d 0.861
f_dihedral_angle_d 14.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2620
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 110

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
HKL-2000 data scaling
PHENIX phasing version: PHASER