X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
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 6.0, 30% PEG 600, 5% PEG 1000, 10% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.41 α = 90
b = 41.93 β = 90
c = 67.16 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
1.28 21.7 99.8 0.067 -- -- 8.2 19067 19067 -3.0 -3.0 11.3
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)
1.28 1.29 98.7 0.507 -- 2.5 8.2 --

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 1.28 21.7 -- 1.35 18922 18922 973 -- -- 0.1644 0.1623 0.2027 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 1.281 1.3485 -- 123 -- 0.2266 0.2745 -- 96.0
X Ray Diffraction 1.3485 1.433 -- 140 -- 0.1721 0.2155 -- 99.0
X Ray Diffraction 1.433 1.5436 -- 134 -- 0.1352 0.1978 -- 99.0
X Ray Diffraction 1.5436 1.6989 -- 142 -- 0.1276 0.1769 -- 99.0
X Ray Diffraction 1.6989 1.9446 -- 137 -- 0.1422 0.2097 -- 100.0
X Ray Diffraction 1.9446 2.4495 -- 146 -- 0.1392 0.1991 -- 100.0
X Ray Diffraction 2.4495 21.7312 -- 151 -- 0.1841 0.2 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 16.1
Anisotropic B[1][1] -2.2304
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.0929
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1375
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.088
f_angle_d 1.535
f_bond_d 0.016
f_dihedral_angle_d 15.475
f_plane_restr 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 762
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 60

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