X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Temperature 293.0
Details 12% PEG-8000, 0.2 M Ammonium Sulphate 2% PEG-400, 1% 1,2,3 heptanetriol, 1 mM Sodium Tungstate, 0.1 M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.36 α = 90
b = 105.83 β = 90
c = 208.71 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2003-01-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, HAMBURG BW7B

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
3.1 20 96.0 0.048 -- -- 3.7 -- 33285 -- -- 101.02
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)
3.1 3.2 96.0 0.38 -- 2.1 3.2 --

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 3.1 14.976 -- 1.38 -- 31869 1588 96.04 -- 0.2283 0.2266 0.2592 --
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 3.1 3.1991 -- 148 2706 0.4083 0.4465 -- 96.0
X Ray Diffraction 3.1991 3.3123 -- 126 2710 0.3694 0.4041 -- 96.0
X Ray Diffraction 3.3123 3.4434 -- 140 2706 0.3284 0.3292 -- 96.0
X Ray Diffraction 3.4434 3.598 -- 148 2732 0.288 0.3504 -- 96.0
X Ray Diffraction 3.598 3.7848 -- 137 2731 0.2746 0.2937 -- 96.0
X Ray Diffraction 3.7848 4.0177 -- 166 2707 0.2366 0.2562 -- 96.0
X Ray Diffraction 4.0177 4.3209 -- 134 2762 0.2044 0.2395 -- 96.0
X Ray Diffraction 4.3209 4.7432 -- 146 2772 0.1747 0.2435 -- 96.0
X Ray Diffraction 4.7432 5.4011 -- 137 2774 0.172 0.2028 -- 96.0
X Ray Diffraction 5.4011 6.7018 -- 159 2807 0.1992 0.2415 -- 96.0
X Ray Diffraction 6.7018 14.9762 -- 147 2874 0.1964 0.2195 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 56.3438
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -40.0922
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -16.2516
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.112
f_angle_d 1.497
f_dihedral_angle_d 26.624
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8235
Nucleic Acid Atoms 0
Heterogen Atoms 99
Solvent Atoms 8

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
MAR345dtb data collection
Phaser model building
PHENIX version: (phenix.refine) refinement