X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.15
Details 15% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.3 α = 90
b = 71.4 β = 100.3
c = 72.4 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Collimating mirror 2009-08-01
Diffraction Radiation
Monochromator Protocol
Bartels Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA

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
1.51 50 99.9 -- 0.051 -- 3.7 55139 55139 -- -- 12.89
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)
1.51 1.54 99.6 -- 0.487 2.7 3.5 2742

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 1.51 35.617 -- 0.0 55377 52718 2659 95.43 0.1555 0.1555 0.1547 0.1715 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 1.5101 1.5641 -- 256 4539 0.2155 0.2405 -- 87.0
X Ray Diffraction 1.5641 1.6267 -- 252 4674 0.1862 0.2309 -- 90.0
X Ray Diffraction 1.6267 1.7007 -- 262 4806 0.1679 0.1869 -- 92.0
X Ray Diffraction 1.7007 1.7904 -- 282 4968 0.1513 0.1647 -- 95.0
X Ray Diffraction 1.7904 1.9026 -- 299 4942 0.1419 0.1605 -- 96.0
X Ray Diffraction 1.9026 2.0494 -- 249 5113 0.1397 0.1644 -- 98.0
X Ray Diffraction 2.0494 2.2556 -- 250 5253 0.144 0.1753 -- 99.0
X Ray Diffraction 2.2556 2.582 -- 273 5190 0.1529 0.183 -- 99.0
X Ray Diffraction 2.582 3.2527 -- 271 5244 0.1641 0.1766 -- 99.0
X Ray Diffraction 3.2527 35.6265 -- 265 5330 0.149 0.1493 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.1242
Anisotropic B[1][1] 2.3278
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.2716
Anisotropic B[2][2] -2.0029
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.3249
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.741
f_plane_restr 0.005
f_chiral_restr 0.075
f_angle_d 1.114
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2344
Nucleic Acid Atoms 0
Heterogen Atoms 93
Solvent Atoms 347

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.4_486) refinement
PHASER model building
MAR345dtb data collection