X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 278.0
Details 21% PEG 3350, 250 mM ammonium formate pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 175.88 α = 90
b = 175.88 β = 90
c = 81.42 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 K-B pair of biomorph mirrors 2013-08-14
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D

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
3 50 94.3 0.07 -- -- 2.0 19002 17731 0.0 0.0 73.7
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)
3.0 3.18 95.1 0.613 -- 1.3 2.0 2893

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 3.0005 47.006 -- 1.37 19002 17724 1836 94.23 -- 0.1922 0.1847 0.2175 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 3.0005 3.0816 -- 140 1235 0.3137 0.3175 -- 83.0
X Ray Diffraction 3.0816 3.1722 -- 140 1252 0.2767 0.3318 -- 87.0
X Ray Diffraction 3.1722 3.2746 -- 139 1235 0.2556 0.2673 -- 87.0
X Ray Diffraction 3.2746 3.3916 -- 142 1308 0.2501 0.2811 -- 88.0
X Ray Diffraction 3.3916 3.5273 -- 142 1243 0.2416 0.2644 -- 86.0
X Ray Diffraction 3.5273 3.6878 -- 117 1053 0.3309 0.3531 -- 74.0
X Ray Diffraction 3.6878 3.8822 -- 121 1139 0.2186 0.241 -- 79.0
X Ray Diffraction 3.8822 4.1253 -- 138 1223 0.1746 0.2139 -- 84.0
X Ray Diffraction 4.1253 4.4436 -- 133 1227 0.1572 0.197 -- 86.0
X Ray Diffraction 4.4436 4.8903 -- 135 1274 0.1471 0.1499 -- 87.0
X Ray Diffraction 4.8903 5.597 -- 144 1244 0.1516 0.1688 -- 87.0
X Ray Diffraction 5.597 7.0478 -- 139 1259 0.1518 0.208 -- 87.0
X Ray Diffraction 7.0478 47.0119 -- 143 1259 0.1507 0.2024 -- 87.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 88.5512
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.102
f_plane_restr 0.002
f_bond_d 0.004
f_chiral_restr 0.046
f_angle_d 0.712
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5098
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.14
Blu-Ice data collection