X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.97
Temperature 293.0
Details 0.1 microliters protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 0.1-0.2 microliters crystallization buffer (0.1 M MES pH 5.97, 30% PEG 600, 7.5% PEG 1000, 5% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.26 α = 90
b = 33.03 β = 90
c = 42.92 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 300 mm CCD -- 2010-11-11
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.9794 APS 23-ID-B

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
0.98 18.18 97.2 0.091 -- -- 10.0 20751 20751 -3.0 -3.0 7.3
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)
0.98 0.99 77.6 0.214 -- 5.4 3.6 --

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 0.98 18.18 -- 1.34 20588 20588 1057 96.67 -- 0.0948 0.0938 0.1134 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 0.9794 1.0239 -- 95 2199 0.1102 0.1359 -- 88.0
X Ray Diffraction 1.0239 1.0779 -- 131 2405 0.0851 0.1133 -- 97.0
X Ray Diffraction 1.0779 1.1454 -- 124 2426 0.0727 0.0985 -- 96.0
X Ray Diffraction 1.1454 1.2339 -- 151 2421 0.0712 0.0982 -- 98.0
X Ray Diffraction 1.2339 1.358 -- 128 2457 0.0728 0.1009 -- 98.0
X Ray Diffraction 1.358 1.5544 -- 163 2461 0.0774 0.0985 -- 99.0
X Ray Diffraction 1.5544 1.958 -- 131 2557 0.0854 0.1076 -- 100.0
X Ray Diffraction 1.958 18.1809 -- 134 2605 0.1204 0.1326 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Anisotropic B[1][1] -1.7181
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0614
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.7795
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.091
f_plane_restr 0.011
f_bond_d 0.017
f_angle_d 1.64
f_dihedral_angle_d 16.948
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 386
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 52

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.7.3_927)
HKL-2000 data reduction
HKL-2000 data scaling