X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details 30% PEG-MME2000, 0.1M potasiumm thiocyanate, 1.0% benzamidine-HCl, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.53 α = 90
b = 89.53 β = 90
c = 89.53 γ = 90
Symmetry
Space Group P 42 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARCCD -- 2010-10-18
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00150 SLS X06DA

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
2.12 89.53 99.5 -- 0.089 -- 9.9 7429 7429 1.45 1.1 --
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)
2.12 2.23 97.1 0.691 0.691 1.1 7.8 1020

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 2.12 44.764 -- 1.46 13112 7403 642 99.18 -- 0.1959 0.1937 0.238 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 2.12 2.2826 -- 129 2425 0.3144 0.3859 -- 96.0
X Ray Diffraction 2.2826 2.5123 -- 125 2502 0.2161 0.2613 -- 100.0
X Ray Diffraction 2.5123 2.8758 -- 125 2516 0.1978 0.2645 -- 100.0
X Ray Diffraction 2.8758 3.623 -- 135 2510 0.1848 0.2256 -- 100.0
X Ray Diffraction 3.623 44.774 -- 128 2517 0.1593 0.1831 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.7094
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.345
f_plane_restr 0.003
f_chiral_restr 0.064
f_angle_d 1.033
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 914
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 89

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.9 data reduction
Mosflm data collection