X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1 M Imidazol pH 6.5, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.12 α = 90
b = 78.77 β = 99.93
c = 69.49 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-08-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.25 28.24 99.7 -- 0.052 -- 3.7 190028 190028 -3.0 -3.0 9.7
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)
1.25 1.28 99.7 -- 0.674 2.33 3.4 14021

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 1.25 28.24 -- 0.0 190020 190020 9556 99.76 -- 0.1689 0.1682 0.182 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 1.25 1.2642 5972 315 5972 0.2936 0.2827 -- 100.0
X Ray Diffraction 1.2642 1.2791 6020 309 6020 0.258 0.2563 -- 100.0
X Ray Diffraction 1.2791 1.2947 5985 349 5985 0.2453 0.2638 -- 100.0
X Ray Diffraction 1.2947 1.3111 6060 275 6060 0.2291 0.2429 -- 100.0
X Ray Diffraction 1.3111 1.3283 5979 320 5979 0.219 0.2359 -- 100.0
X Ray Diffraction 1.3283 1.3465 5992 300 5992 0.2168 0.2218 -- 100.0
X Ray Diffraction 1.3465 1.3657 5981 334 5981 0.2083 0.2343 -- 100.0
X Ray Diffraction 1.3657 1.3861 6045 294 6045 0.1966 0.2111 -- 100.0
X Ray Diffraction 1.3861 1.4078 5989 315 5989 0.1909 0.1897 -- 100.0
X Ray Diffraction 1.4078 1.4309 5976 333 5976 0.1892 0.2293 -- 100.0
X Ray Diffraction 1.4309 1.4555 6008 318 6008 0.1828 0.215 -- 100.0
X Ray Diffraction 1.4555 1.482 6027 341 6027 0.1776 0.1823 -- 100.0
X Ray Diffraction 1.482 1.5105 5953 339 5953 0.1675 0.1991 -- 100.0
X Ray Diffraction 1.5105 1.5413 6010 324 6010 0.1595 0.1765 -- 100.0
X Ray Diffraction 1.5413 1.5749 6004 306 6004 0.1557 0.1695 -- 100.0
X Ray Diffraction 1.5749 1.6115 6029 321 6029 0.1539 0.186 -- 100.0
X Ray Diffraction 1.6115 1.6518 5971 336 5971 0.1575 0.1915 -- 100.0
X Ray Diffraction 1.6518 1.6964 6017 336 6017 0.1537 0.1664 -- 100.0
X Ray Diffraction 1.6964 1.7464 6045 282 6045 0.1504 0.1537 -- 100.0
X Ray Diffraction 1.7464 1.8027 5998 322 5998 0.1487 0.1708 -- 100.0
X Ray Diffraction 1.8027 1.8671 5986 331 5986 0.1492 0.1537 -- 100.0
X Ray Diffraction 1.8671 1.9419 6008 337 6008 0.1558 0.177 -- 100.0
X Ray Diffraction 1.9419 2.0302 6047 310 6047 0.1532 0.1677 -- 100.0
X Ray Diffraction 2.0302 2.1372 6017 296 6017 0.1493 0.16 -- 100.0
X Ray Diffraction 2.1372 2.2711 6042 321 6042 0.1579 0.17 -- 100.0
X Ray Diffraction 2.2711 2.4463 5987 348 5987 0.1572 0.1763 -- 100.0
X Ray Diffraction 2.4463 2.6923 6059 311 6059 0.1658 0.1695 -- 100.0
X Ray Diffraction 2.6923 3.0815 6049 309 6049 0.1723 0.1851 -- 100.0
X Ray Diffraction 3.0815 3.8808 6074 317 6074 0.1606 0.1766 -- 100.0
X Ray Diffraction 3.8808 28.2475 6134 307 6134 0.1644 0.171 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic, TLS
Mean Isotropic B 19.617
Anisotropic B[1][1] -0.6886
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.6778
Anisotropic B[2][2] -0.3199
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.0085
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.011
f_chiral_restr 0.121
f_dihedral_angle_d 13.021
f_angle_d 1.758
f_bond_d 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4814
Nucleic Acid Atoms 0
Heterogen Atoms 130
Solvent Atoms 803

Software

Computing
Computing Package Purpose
SERGUI Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER (2.1.4) 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 version: (2.1.4) model building
SERGUI data collection