X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 289.0
Details 1M sodium/potassium phosphate buffer

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.39 α = 90
b = 160.05 β = 90
c = 209.91 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-12-16
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID

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
2.6 50 98.4 0.104 -- 25.413 6.4 47865 47865 0.0 0.0 52.68
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)
2.6 2.64 95.8 0.969 -- 1.94 5.7 2328

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
SAD 2.6 42.281 -- 1.35 -- 47775 2410 97.27 -- 0.1999 0.198 0.238 --
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 2.583 2.6358 -- 122 2126 0.265 0.2966 -- 79.0
X Ray Diffraction 2.6358 2.6931 -- 156 2570 0.2563 0.3122 -- 96.0
X Ray Diffraction 2.6931 2.7557 -- 105 2644 0.2308 0.2233 -- 96.0
X Ray Diffraction 2.7557 2.8246 -- 112 2658 0.2411 0.2735 -- 97.0
X Ray Diffraction 2.8246 2.9009 -- 159 2650 0.2569 0.3507 -- 97.0
X Ray Diffraction 2.9009 2.9863 -- 147 2620 0.2824 0.3879 -- 97.0
X Ray Diffraction 2.9863 3.0826 -- 146 2666 0.2727 0.2996 -- 98.0
X Ray Diffraction 3.0826 3.1928 -- 119 2722 0.228 0.3184 -- 99.0
X Ray Diffraction 3.1928 3.3206 -- 140 2674 0.2302 0.2867 -- 99.0
X Ray Diffraction 3.3206 3.4716 -- 127 2728 0.2159 0.28 -- 99.0
X Ray Diffraction 3.4716 3.6546 -- 209 2640 0.2095 0.279 -- 99.0
X Ray Diffraction 3.6546 3.8834 -- 160 2722 0.188 0.2161 -- 99.0
X Ray Diffraction 3.8834 4.183 -- 114 2751 0.1666 0.2251 -- 100.0
X Ray Diffraction 4.183 4.6035 -- 158 2725 0.1473 0.1813 -- 99.0
X Ray Diffraction 4.6035 5.2685 -- 151 2761 0.1464 0.1871 -- 100.0
X Ray Diffraction 5.2685 6.6337 -- 157 2801 0.1853 0.2015 -- 100.0
X Ray Diffraction 6.6337 42.2865 -- 128 2907 0.1997 0.1899 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.9023
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_dihedral_angle_d 12.256
f_angle_d 0.725
f_bond_d 0.003
f_chiral_restr 0.047
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4899
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 174

Software

Software
Software Name Purpose
HKL-3000 data reduction
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
PDB_EXTRACT data extraction version: 3.15
HKL-3000 data scaling
HKL-3000 phasing