X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details 22% Polyacrylic acid 5100, 20 mM MgCl2, 0.1 M CHES/NaOH pH 9.0, 4% (v/v) 2,5 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.12 α = 90
b = 139.07 β = 90
c = 174.88 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 MARMOSAIC 225 mm CCD mirrors 2012-03-13
Diffraction Radiation
Monochromator Protocol
Si-111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1

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
2.94 46.36 96.4 -- 0.087 -- 3.6 43049 43049 -- -- --
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)
2.94 3.1 84.5 0.545 0.545 1.4 3.3 5413

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 2.941 45.853 -- 0.0 -- 43006 2149 95.83 -- 0.2214 0.2203 0.2428 --
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 2.9411 3.0095 -- 117 2327 0.3579 0.3804 -- 83.0
X Ray Diffraction 3.0095 3.0848 -- 125 2347 0.3357 0.3864 -- 84.0
X Ray Diffraction 3.0848 3.1682 -- 142 2672 0.3105 0.3262 -- 95.0
X Ray Diffraction 3.1682 3.2614 -- 146 2774 0.2919 0.3112 -- 99.0
X Ray Diffraction 3.2614 3.3666 -- 145 2763 0.2759 0.2928 -- 99.0
X Ray Diffraction 3.3666 3.4869 -- 147 2772 0.248 0.2837 -- 99.0
X Ray Diffraction 3.4869 3.6265 -- 144 2765 0.2351 0.2937 -- 99.0
X Ray Diffraction 3.6265 3.7914 -- 149 2804 0.2206 0.2471 -- 98.0
X Ray Diffraction 3.7914 3.9912 -- 146 2782 0.2186 0.2633 -- 98.0
X Ray Diffraction 3.9912 4.2411 -- 145 2775 0.1905 0.233 -- 98.0
X Ray Diffraction 4.2411 4.5683 -- 148 2778 0.1748 0.1845 -- 98.0
X Ray Diffraction 4.5683 5.0275 -- 147 2796 0.1661 0.2 -- 98.0
X Ray Diffraction 5.0275 5.7538 -- 148 2801 0.226 0.2374 -- 98.0
X Ray Diffraction 5.7538 7.2446 -- 148 2824 0.2591 0.2741 -- 97.0
X Ray Diffraction 7.2446 45.8586 -- 152 2877 0.1753 0.1784 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.0633
Anisotropic B[1][1] -5.9326
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.908
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.8406
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.431
f_plane_restr 0.004
f_chiral_restr 0.057
f_angle_d 0.884
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8595
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.16 data reduction
Mosflm data collection