X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 282.0
Details Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5) and 100 mM NaCl. Mother liqueur contained 1.7 M ammonium sulfate, 0.085 M Hepes (pH 7.5), 1.7% PEG 400 and 15% glycerol, vapor diffusion, sitting drop, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.49 α = 90
b = 92.49 β = 90
c = 136 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2012-04-02
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
1.9 30 99.9 -- 0.09 -- -- -- 53597 0.0 -3.0 27.297
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)
1.9 1.95 99.9 0.611 -- 2.55 -- --

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 1.9 29.551 -- 2.02 53647 53593 2679 99.94 -- 0.1496 0.1484 0.1728 random
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 1.9001 1.9346 -- 140 2666 0.2092 0.2514 -- 100.0
X Ray Diffraction 1.9346 1.9718 -- 139 2639 0.1986 0.244 -- 100.0
X Ray Diffraction 1.9718 2.0121 -- 139 2645 0.1871 0.2495 -- 100.0
X Ray Diffraction 2.0121 2.0558 -- 140 2660 0.1676 0.2108 -- 100.0
X Ray Diffraction 2.0558 2.1036 -- 139 2636 0.1593 0.1867 -- 100.0
X Ray Diffraction 2.1036 2.1562 -- 139 2634 0.1459 0.1979 -- 100.0
X Ray Diffraction 2.1562 2.2145 -- 139 2648 0.144 0.1731 -- 100.0
X Ray Diffraction 2.2145 2.2796 -- 139 2642 0.1404 0.193 -- 100.0
X Ray Diffraction 2.2796 2.3532 -- 141 2688 0.1387 0.1843 -- 100.0
X Ray Diffraction 2.3532 2.4373 -- 140 2648 0.1416 0.179 -- 100.0
X Ray Diffraction 2.4373 2.5348 -- 140 2671 0.1421 0.1757 -- 100.0
X Ray Diffraction 2.5348 2.6501 -- 141 2665 0.146 0.1644 -- 100.0
X Ray Diffraction 2.6501 2.7897 -- 140 2675 0.1486 0.178 -- 100.0
X Ray Diffraction 2.7897 2.9643 -- 141 2673 0.1622 0.1912 -- 100.0
X Ray Diffraction 2.9643 3.193 -- 142 2705 0.1557 0.1653 -- 100.0
X Ray Diffraction 3.193 3.5138 -- 142 2690 0.1481 0.1539 -- 100.0
X Ray Diffraction 3.5138 4.0212 -- 144 2727 0.1309 0.1494 -- 100.0
X Ray Diffraction 4.0212 5.0622 -- 144 2735 0.119 0.1323 -- 100.0
X Ray Diffraction 5.0622 29.5547 -- 150 2867 0.1579 0.1601 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.6144
Anisotropic B[1][1] -0.0825
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.0825
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.165
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.0
f_plane_restr 0.004
f_chiral_restr 0.072
f_angle_d 1.105
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3758
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 471

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction