X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 296.0
Details 23-34% PAA-5100, 100mM HEPES (pH 7.5), 20mM MgCl2, 0.6% BoG

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.94 α = 90
b = 132.23 β = 90
c = 180.46 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2012-09-12
Diffraction Radiation
Monochromator Protocol
Horizontal focusing 5.05iN asymmetric cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.97590 CHESS A1

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
1.81 40 98.43 0.056 -- 22.395 4.7 128926 128926 -- -3.0 24.49
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)
1.81 1.875 90.8 0.4037 -- 2.49 2.49 5835

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 1.81 35.55 -- -- -- 128316 6401 98.0 -- 0.162 0.16 0.197 Random selection
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 1.81 1.8311 -- 202 3565 0.2366 0.2642 -- 88.0
X Ray Diffraction 1.8311 1.8527 -- 170 3800 0.2285 0.2648 -- 92.0
X Ray Diffraction 1.8527 1.8753 -- 175 3845 0.2207 0.2945 -- 93.0
X Ray Diffraction 1.8753 1.899 -- 180 3923 0.2102 0.2417 -- 95.0
X Ray Diffraction 1.899 1.924 -- 157 3950 0.2022 0.2614 -- 95.0
X Ray Diffraction 1.924 1.9503 -- 226 3970 0.1936 0.2552 -- 96.0
X Ray Diffraction 1.9503 1.9782 -- 218 4030 0.1885 0.2306 -- 98.0
X Ray Diffraction 1.9782 2.0077 -- 211 4087 0.1792 0.2414 -- 99.0
X Ray Diffraction 2.0077 2.0391 -- 212 4107 0.1799 0.2266 -- 100.0
X Ray Diffraction 2.0391 2.0725 -- 242 4082 0.1786 0.2157 -- 100.0
X Ray Diffraction 2.0725 2.1083 -- 216 4101 0.177 0.1995 -- 99.0
X Ray Diffraction 2.1083 2.1466 -- 205 4098 0.1726 0.2271 -- 100.0
X Ray Diffraction 2.1466 2.1879 -- 225 4122 0.1729 0.2195 -- 99.0
X Ray Diffraction 2.1879 2.2325 -- 234 4076 0.1711 0.2467 -- 99.0
X Ray Diffraction 2.2325 2.2811 -- 227 4075 0.1679 0.2198 -- 99.0
X Ray Diffraction 2.2811 2.3341 -- 200 4085 0.1662 0.2228 -- 99.0
X Ray Diffraction 2.3341 2.3925 -- 204 4127 0.1635 0.2058 -- 99.0
X Ray Diffraction 2.3925 2.4571 -- 233 4074 0.1663 0.2163 -- 99.0
X Ray Diffraction 2.4571 2.5294 -- 225 4080 0.1624 0.2106 -- 99.0
X Ray Diffraction 2.5294 2.611 -- 216 4100 0.1724 0.2201 -- 99.0
X Ray Diffraction 2.611 2.7043 -- 251 4109 0.1683 0.2019 -- 99.0
X Ray Diffraction 2.7043 2.8126 -- 243 4061 0.1592 0.1944 -- 99.0
X Ray Diffraction 2.8126 2.9405 -- 231 4118 0.1651 0.2189 -- 99.0
X Ray Diffraction 2.9405 3.0955 -- 224 4129 0.1685 0.2262 -- 99.0
X Ray Diffraction 3.0955 3.2893 -- 223 4152 0.159 0.1945 -- 100.0
X Ray Diffraction 3.2893 3.543 -- 240 4121 0.1486 0.1815 -- 99.0
X Ray Diffraction 3.543 3.8992 -- 235 4149 0.1359 0.1639 -- 99.0
X Ray Diffraction 3.8992 4.4625 -- 219 4188 0.1288 0.1632 -- 100.0
X Ray Diffraction 4.4625 5.6186 -- 194 4258 0.1329 0.1593 -- 100.0
X Ray Diffraction 5.6186 35.5604 -- 163 4333 0.1631 0.154 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.97
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.31
f_chiral_restr 0.061
f_bond_d 0.013
f_plane_restr 0.007
f_dihedral_angle_d 14.929
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.188
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 72
Solvent Atoms 1128

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE: 1.8.4_1496)
HKL-2000 data collection version: v704u
HKL-2000 data reduction version: v704u
PHASER phasing version: 2.5.6
PDB_EXTRACT data extraction version: 3.14
Coot model building version: 0.7.2
PHASER model building