X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details 0.2 M ammonium sulfate, 0.1 M sodium citrate:HCl, pH 5.6, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.71 α = 90
b = 80.82 β = 90
c = 88.05 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 ADSC QUANTUM 315r -- 2012-10-03
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 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
1.48 59.54 87.7 0.076 -- -- 7.8 76480 67101 -- -- --
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)
1.48 1.51 94.9 -- -- -- -- --

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 1.48 36.219 -- 1.34 -- 67030 3339 87.73 -- 0.187 0.1857 0.2113 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 1.48 1.5009 -- 153 2784 0.1996 0.2284 -- 94.0
X Ray Diffraction 1.5009 1.5233 -- 145 2874 0.1885 0.2376 -- 95.0
X Ray Diffraction 1.5233 1.5471 -- 159 2835 0.1841 0.2301 -- 95.0
X Ray Diffraction 1.5471 1.5725 -- 132 2880 0.1789 0.1899 -- 95.0
X Ray Diffraction 1.5725 1.5996 -- 156 2840 0.1685 0.2006 -- 96.0
X Ray Diffraction 1.5996 1.6287 -- 137 2884 0.1723 0.2086 -- 96.0
X Ray Diffraction 1.6287 1.66 -- 147 2867 0.1707 0.184 -- 96.0
X Ray Diffraction 1.66 1.6939 -- 151 2889 0.1738 0.208 -- 96.0
X Ray Diffraction 1.6939 1.7307 -- 147 2884 0.1749 0.2129 -- 96.0
X Ray Diffraction 1.7307 1.771 -- 154 2901 0.177 0.2211 -- 97.0
X Ray Diffraction 1.771 1.8153 -- 147 2898 0.174 0.1826 -- 97.0
X Ray Diffraction 1.8153 1.8644 -- 165 2907 0.1809 0.2148 -- 97.0
X Ray Diffraction 1.8644 1.9192 -- 64 1273 0.2015 0.2464 -- 84.0
X Ray Diffraction 1.9192 1.9812 -- 115 1941 0.2044 0.217 -- 77.0
X Ray Diffraction 1.9812 2.052 -- 141 2955 0.1912 0.2311 -- 97.0
X Ray Diffraction 2.052 2.1341 -- 154 2942 0.1809 0.2183 -- 98.0
X Ray Diffraction 2.1341 2.2312 -- 125 2393 0.1806 0.188 -- 89.0
X Ray Diffraction 2.2312 2.3488 -- 90 1463 0.1931 0.2337 -- 90.0
X Ray Diffraction 2.3488 2.496 -- 161 2973 0.1838 0.2315 -- 98.0
X Ray Diffraction 2.496 2.6886 -- 141 3023 0.19 0.1909 -- 98.0
X Ray Diffraction 2.6886 2.9591 -- 149 3039 0.1912 0.2264 -- 99.0
X Ray Diffraction 2.9591 3.387 -- 171 3032 0.1924 0.2118 -- 99.0
X Ray Diffraction 3.387 4.2662 -- 58 1080 0.1682 0.1889 -- 35.0
X Ray Diffraction 4.2662 36.2294 -- 177 3134 0.193 0.2054 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.071
f_dihedral_angle_d 12.335
f_angle_d 1.075
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3349
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 310

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
MOLREP model building
CBASS data collection