X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Chloride, 0.1M Bis-Tris:HCl, pH 6.5); Cryoprotection (Reservoir + final concentration of 20%(v/v) Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.19 α = 90
b = 35.19 β = 90
c = 205.33 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRRORS 2013-02-07
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A

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
2.25 50 97.3 0.069 -- -- 9.0 11848 11529 -- -- --
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)
2.25 2.29 100.0 0.262 -- -- 9.5 585

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 2.25 35.193 -- 1.42 -- 11454 541 97.24 -- 0.2257 0.2222 0.2921 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 2.2529 2.4788 -- 125 2805 0.2551 0.301 -- 96.0
X Ray Diffraction 2.4788 2.8356 -- 147 2740 0.2463 0.2878 -- 95.0
X Ray Diffraction 2.8356 3.5657 -- 140 2800 0.2336 0.3208 -- 94.0
X Ray Diffraction 3.5657 15.6931 -- 128 2520 0.1907 0.2766 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.2146
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.216
f_plane_restr 0.008
f_chiral_restr 0.055
f_angle_d 1.488
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1722
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 1

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.2_1309) Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction