X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details Protein Solution (6.8-13.5 mg/ml protein, 25mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.4M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 5.6) Cryoprotected with 20% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 151.3 α = 90
b = 151.3 β = 90
c = 221.15 γ = 120
Symmetry
Space Group P 65 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 -- 2012-03-08
CCD MARMOSAIC 300 mm CCD -- 2012-02-11
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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
2.21 50 98.7 0.118 -- -- 19.9 75422 74442 0.0 0.0 42.94
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)
2.21 2.25 76.6 -- -- -- 9.2 2830

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 2.214 49.526 -- 1.34 74655 74289 3730 99.51 -- 0.2 0.199 0.2201 RAMDOM, 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 2.2142 2.2422 -- 180 2274 0.3097 0.3698 -- 91.0
X Ray Diffraction 2.2422 2.2717 -- -- 2680 0.2835 -- -- 98.0
X Ray Diffraction 2.2717 2.3029 -- 184 2506 0.2698 0.3106 -- 99.0
X Ray Diffraction 2.3029 2.3358 -- 187 2504 0.2651 0.2852 -- 100.0
X Ray Diffraction 2.3358 2.3706 -- 187 2543 0.2505 0.288 -- 100.0
X Ray Diffraction 2.3706 2.4077 -- -- 2722 0.2387 -- -- 100.0
X Ray Diffraction 2.4077 2.4471 -- 187 2543 0.2341 0.2831 -- 100.0
X Ray Diffraction 2.4471 2.4893 -- 187 2517 0.2286 0.2678 -- 100.0
X Ray Diffraction 2.4893 2.5346 -- 187 2542 0.2244 0.3007 -- 100.0
X Ray Diffraction 2.5346 2.5833 -- -- 2736 0.2209 -- -- 100.0
X Ray Diffraction 2.5833 2.6361 -- 187 2549 0.22 0.2635 -- 100.0
X Ray Diffraction 2.6361 2.6934 -- 187 2528 0.2148 0.2483 -- 100.0
X Ray Diffraction 2.6934 2.756 -- 54 2701 0.2102 0.2518 -- 100.0
X Ray Diffraction 2.756 2.825 -- 133 2599 0.2171 0.2711 -- 100.0
X Ray Diffraction 2.825 2.9013 -- 187 2573 0.208 0.2504 -- 100.0
X Ray Diffraction 2.9013 2.9867 -- 187 2560 0.2134 0.2145 -- 100.0
X Ray Diffraction 2.9867 3.0831 -- -- 2751 0.2093 -- -- 100.0
X Ray Diffraction 3.0831 3.1932 -- 187 2566 0.2077 0.2452 -- 100.0
X Ray Diffraction 3.1932 3.3211 -- 187 2567 0.1989 0.2403 -- 100.0
X Ray Diffraction 3.3211 3.4722 -- 187 2582 0.1934 0.2302 -- 100.0
X Ray Diffraction 3.4722 3.6552 -- -- 2778 0.1817 -- -- 100.0
X Ray Diffraction 3.6552 3.8841 -- 187 2605 0.1813 0.1967 -- 100.0
X Ray Diffraction 3.8841 4.1839 -- 187 2611 0.1643 0.1824 -- 100.0
X Ray Diffraction 4.1839 4.6046 -- 187 2627 0.1601 0.1754 -- 100.0
X Ray Diffraction 4.6046 5.2703 -- -- 2846 0.1596 -- -- 100.0
X Ray Diffraction 5.2703 6.6375 -- 187 2684 0.2198 0.186 -- 100.0
X Ray Diffraction 6.6375 49.5382 -- 187 2865 0.2098 0.1942 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.372
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.725
f_plane_restr 0.002
f_chiral_restr 0.048
f_angle_d 0.685
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6192
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 304

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX: PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction