X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details 100 mM MES, pH 6.2, 18% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.32 α = 90
b = 62.04 β = 90
c = 84.22 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 Vertical Focusing Mirror: ultra-low expansion (ULE) titanium silicate flat mirror with Pt, uncoated, and Pd strips 2011-06-29
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 1.28243, 1.28289, 1.27347 CLSI 08ID-1

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
1.45 31.11 99.4 0.049 -- -- 8.7 36356 36344 1.0 2.5 --
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)
1.45 1.53 96.2 0.205 -- 7.1 6.9 5029

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
MAD 1.45 31.02 -- 1.05 36344 36216 1994 99.55 -- 0.1612 0.1602 0.1781 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 1.45 1.4863 -- 134 2289 0.2763 0.3167 -- 95.0
X Ray Diffraction 1.4863 1.5264 -- 140 2391 0.2196 0.247 -- 99.0
X Ray Diffraction 1.5264 1.5714 -- 139 2400 0.1867 0.2044 -- 100.0
X Ray Diffraction 1.5714 1.6221 -- 143 2438 0.1664 0.2142 -- 100.0
X Ray Diffraction 1.6221 1.68 -- 140 2422 0.1613 0.2014 -- 100.0
X Ray Diffraction 1.68 1.7473 -- 142 2451 0.1555 0.1833 -- 100.0
X Ray Diffraction 1.7473 1.8268 -- 142 2431 0.1534 0.1892 -- 100.0
X Ray Diffraction 1.8268 1.9231 -- 141 2426 0.1522 0.1676 -- 100.0
X Ray Diffraction 1.9231 2.0436 -- 142 2427 0.1516 0.1612 -- 100.0
X Ray Diffraction 2.0436 2.2013 -- 143 2451 0.1443 0.1878 -- 100.0
X Ray Diffraction 2.2013 2.4228 -- 144 2480 0.1485 0.1477 -- 100.0
X Ray Diffraction 2.4228 2.7732 -- 144 2471 0.1476 0.1604 -- 100.0
X Ray Diffraction 2.7732 3.4932 -- 147 2520 0.1552 0.1635 -- 100.0
X Ray Diffraction 3.4932 31.0271 -- 153 2625 0.1667 0.1825 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -3.6234
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.8156
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.1922
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.077
f_dihedral_angle_d 11.682
f_angle_d 1.413
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1531
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 260

Software

Computing
Computing Package Purpose
MxDC Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX (phenix.autosol: 1.7.1_743)) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.autosol: 1.7.1_743)) model building
MxDC data collection