X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 7% PEG 4000, 0.5M NaCl, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.09 α = 90
b = 117.09 β = 90
c = 321.38 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2008-11-12
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25

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
2.26 48.35 98.7643 0.12 -- -- 2.3 229990 227148 0.0 0.0 --
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)
2.26 2.3 72.0 -- -- 1.06 1.7 --

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 2.2629 47.3159 -- 0.05 229986 200267 10883 87.0779 -- 0.1757 0.1724 0.227 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 2.2916 2.3297 -- 577 6992 0.2722 0.3242 -- 65.0
X Ray Diffraction 2.3297 2.3705 -- 569 7358 0.2674 0.3077 -- 70.0
X Ray Diffraction 2.3705 2.4144 -- 600 7624 0.256 0.302 -- 71.0
X Ray Diffraction 2.4144 2.4616 -- 0 8413 0.2525 0.0 -- 79.0
X Ray Diffraction 2.4616 2.5128 -- 604 7956 0.2409 0.298 -- 74.0
X Ray Diffraction 2.5128 2.5686 -- 629 8054 0.2354 0.2922 -- 75.0
X Ray Diffraction 2.5686 2.6296 -- 0 8932 0.2277 0.0 -- 83.0
X Ray Diffraction 2.6296 2.6969 -- 627 8465 0.2229 0.2842 -- 80.0
X Ray Diffraction 2.6969 2.7717 -- 665 8625 0.2126 0.2674 -- 80.0
X Ray Diffraction 2.7717 2.8555 -- 167 9244 0.2065 0.2416 -- 86.0
X Ray Diffraction 2.8555 2.9505 -- 501 9149 0.1961 0.2693 -- 86.0
X Ray Diffraction 2.9505 3.0596 -- 683 9083 0.1887 0.2499 -- 85.0
X Ray Diffraction 3.0596 3.1867 -- 706 9278 0.1733 0.2148 -- 87.0
X Ray Diffraction 3.1867 3.3381 -- 0 10217 0.1619 0.0 -- 95.0
X Ray Diffraction 3.3381 3.523 -- 734 9593 0.1456 0.2072 -- 90.0
X Ray Diffraction 3.523 3.7572 -- 741 9645 0.1371 0.2034 -- 90.0
X Ray Diffraction 3.7572 4.0695 -- 0 10391 0.1268 0.0 -- 97.0
X Ray Diffraction 4.0695 4.5208 -- 744 9716 0.1117 0.1746 -- 91.0
X Ray Diffraction 4.5208 5.2764 -- 747 9584 0.1213 0.1891 -- 90.0
X Ray Diffraction 5.2764 7.1018 -- 744 9582 0.172 0.2196 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.9812
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.9812
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.9624
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.066
f_dihedral_angle_d 15.252
f_angle_d 1.004
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19557
Nucleic Acid Atoms 0
Heterogen Atoms 96
Solvent Atoms 1867

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
Phaser model building
HKL-2000 data collection