X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 293.0
Details 15 % (w/v) PEG 3350, 0.2M KH2PO4, 3% (w/v) D-trehalose dihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.25 α = 90
b = 136.03 β = 90
c = 81.25 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2010-03-16
Diffraction Radiation
Monochromator Protocol
Si-111 crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2

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 50 99.8 0.064 -- -- -- 51879 51771 3.0 3.0 --
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)
2.0 2.1 99.9 0.49 -- 3.0 -- 6929

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 2.0 41.441 -- 1.99 51771 51768 2589 99.8 -- 0.1636 0.1612 0.208 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 2.0 2.0385 -- 141 2677 0.221 0.2921 -- 100.0
X Ray Diffraction 2.0385 2.0801 -- 142 2697 0.202 0.2775 -- 100.0
X Ray Diffraction 2.0801 2.1253 -- 142 2694 0.1889 0.2559 -- 100.0
X Ray Diffraction 2.1253 2.1747 -- 142 2698 0.1777 0.2378 -- 100.0
X Ray Diffraction 2.1747 2.2291 -- 141 2687 0.1768 0.2449 -- 100.0
X Ray Diffraction 2.2291 2.2894 -- 142 2690 0.1792 0.2559 -- 100.0
X Ray Diffraction 2.2894 2.3567 -- 143 2730 0.1731 0.2322 -- 100.0
X Ray Diffraction 2.3567 2.4328 -- 142 2695 0.1647 0.2413 -- 100.0
X Ray Diffraction 2.4328 2.5197 -- 144 2729 0.1576 0.2251 -- 100.0
X Ray Diffraction 2.5197 2.6206 -- 143 2722 0.1633 0.2411 -- 100.0
X Ray Diffraction 2.6206 2.7399 -- 143 2707 0.1675 0.2357 -- 100.0
X Ray Diffraction 2.7399 2.8843 -- 143 2726 0.1635 0.2205 -- 100.0
X Ray Diffraction 2.8843 3.0649 -- 143 2725 0.1618 0.2136 -- 100.0
X Ray Diffraction 3.0649 3.3015 -- 145 2742 0.1474 0.2063 -- 100.0
X Ray Diffraction 3.3015 3.6336 -- 145 2750 0.1422 0.1739 -- 100.0
X Ray Diffraction 3.6336 4.1589 -- 145 2760 0.1337 0.1703 -- 99.0
X Ray Diffraction 4.1589 5.2382 -- 148 2822 0.124 0.1423 -- 100.0
X Ray Diffraction 5.2382 41.4498 -- 155 2928 0.1836 0.214 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.996
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0046
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.9731
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.01
f_angle_d 1.283
f_dihedral_angle_d 13.537
f_chiral_restr 0.088
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5591
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 481

Software

Software
Software Name Purpose
MAR345 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.6.1_353)
XDS data reduction
XDS data scaling