X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details ~15 mg/mL protein concentration, 1.5 M (NH4)2SO4, 0.11 M Li2SO4, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.58 α = 90
b = 48.7 β = 90
c = 64.88 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
IMAGE PLATE RIGAKU RAXIS IV++ Osmic Confocal Mirrors 2011-12-10
Diffraction Radiation
Monochromator Protocol
Multi-layer mirrors Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.541 -- --

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
1.9 20 97.2 0.095 -- -- 12.3 12143 11803 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)
1.9 1.96 76.2 0.342 -- -- 5.8 756

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 1.901 19.99 -- 2.01 12143 11533 579 95.24 -- 0.1671 0.1647 0.2139 Random 5%
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 1.9008 2.0919 -- 136 2414 0.2011 0.2711 -- 86.0
X Ray Diffraction 2.0919 2.3942 -- 140 2778 0.1413 0.1895 -- 98.0
X Ray Diffraction 2.3942 3.0147 -- 146 2819 0.1543 0.2206 -- 98.0
X Ray Diffraction 3.0147 19.9909 -- 157 2943 0.1712 0.2061 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.2147
Anisotropic B[1][1] 0.0261
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.2013
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.1752
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.639
f_plane_restr 0.006
f_chiral_restr 0.071
f_angle_d 1.066
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 939
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 177

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction