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 = 70.1 α = 90
b = 71.1 β = 100.4
c = 72.7 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Collimating mirror 2009-07-31
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
1.58 50 99.8 -- 0.058 -- 3.8 48248 48248 -- -- 14.2
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)
1.58 1.61 99.6 -- 0.478 3.0 3.7 2403

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 1.58 49.497 -- 0.0 48261 45959 2302 95.53 0.1559 0.1559 0.1547 0.1786 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 1.58 1.6365 -- 191 3987 0.2009 0.2453 -- 88.0
X Ray Diffraction 1.6365 1.702 -- 232 4086 0.1871 0.2441 -- 90.0
X Ray Diffraction 1.702 1.7795 -- 201 4237 0.1637 0.1914 -- 92.0
X Ray Diffraction 1.7795 1.8733 -- 213 4310 0.1516 0.174 -- 95.0
X Ray Diffraction 1.8733 1.9907 -- 257 4344 0.1435 0.1733 -- 96.0
X Ray Diffraction 1.9907 2.1444 -- 226 4476 0.1486 0.1726 -- 98.0
X Ray Diffraction 2.1444 2.3602 -- 236 4516 0.149 0.1763 -- 99.0
X Ray Diffraction 2.3602 2.7017 -- 257 4496 0.1636 0.1947 -- 99.0
X Ray Diffraction 2.7017 3.4037 -- 252 4554 0.1581 0.1726 -- 100.0
X Ray Diffraction 3.4037 49.5213 -- 237 4651 0.1452 0.1617 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.2358
Anisotropic B[1][1] 3.5554
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.1404
Anisotropic B[2][2] -3.5521
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0033
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.736
f_plane_restr 0.005
f_chiral_restr 0.073
f_angle_d 1.081
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2340
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 305

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