X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 291.0
Details 10 mg/mL Se-Met protein, 0.1 M sodium phosphate/citric acid, pH 4.2, 30-40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 291.0
Details 10 mg/mL native protein, 0.1 M sodium phosphate/citric acid, pH 4.2, 30-40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.77 α = 81.84
b = 167 β = 82.17
c = 186.98 γ = 81.44
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Sample to detector distance: 100 to 650 mm, Maximum vertical offset: 200 mm 2011-06-25
PIXEL DECTRIS PILATUS 6M Shutterless data collection, fine phi slicing experiments 2012-08-09
Diffraction Radiation
Monochromator Protocol
Double crystal Si(111) SAD
Liquid nitrogen-cooled double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.97893 SSRL BL9-2
SYNCHROTRON SSRL BEAMLINE BL12-2 0.95369 SSRL BL12-2

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
1.76 39.19 88.0 0.123 0.038 -- 3.6 951878 837015 1.06 0.34 29.29
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)
1.76 1.86 63.9 -- -- 0.4 3.4 --

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 1.8 39.186 -- 1.96 -- 774229 38896 86.87 0.195 0.1898 0.1883 0.2166 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 1.8 1.8205 -- 388 7442 0.3498 0.3717 -- 26.0
X Ray Diffraction 1.8205 1.8419 -- 739 13498 0.3464 0.3708 -- 48.0
X Ray Diffraction 1.8419 1.8643 -- 1013 20431 0.3411 0.3598 -- 72.0
X Ray Diffraction 1.8643 1.8879 -- 1262 24316 0.3401 0.366 -- 86.0
X Ray Diffraction 1.8879 1.9128 -- 1369 25031 0.3269 0.3492 -- 89.0
X Ray Diffraction 1.9128 1.939 -- 1353 25779 0.3112 0.3421 -- 91.0
X Ray Diffraction 1.939 1.9667 -- 1370 25922 0.2981 0.32 -- 92.0
X Ray Diffraction 1.9667 1.996 -- 1376 25864 0.2948 0.3195 -- 92.0
X Ray Diffraction 1.996 2.0272 -- 1358 25717 0.2819 0.3181 -- 91.0
X Ray Diffraction 2.0272 2.0605 -- 1385 25402 0.2773 0.3061 -- 90.0
X Ray Diffraction 2.0605 2.096 -- 1321 24714 0.2669 0.3031 -- 88.0
X Ray Diffraction 2.096 2.1341 -- 1261 23661 0.2452 0.2886 -- 84.0
X Ray Diffraction 2.1341 2.1751 -- 1393 26685 0.223 0.2651 -- 95.0
X Ray Diffraction 2.1751 2.2195 -- 1413 26655 0.2254 0.2562 -- 94.0
X Ray Diffraction 2.2195 2.2678 -- 1380 26335 0.2248 0.2704 -- 93.0
X Ray Diffraction 2.2678 2.3205 -- 1303 26303 0.2104 0.2564 -- 93.0
X Ray Diffraction 2.3205 2.3786 -- 1304 26416 0.2051 0.2556 -- 94.0
X Ray Diffraction 2.3786 2.4429 -- 1417 25959 0.2046 0.252 -- 92.0
X Ray Diffraction 2.4429 2.5147 -- 1321 25295 0.2035 0.2492 -- 90.0
X Ray Diffraction 2.5147 2.5959 -- 1252 23382 0.2071 0.248 -- 83.0
X Ray Diffraction 2.5959 2.6887 -- 1488 26583 0.199 0.242 -- 94.0
X Ray Diffraction 2.6887 2.7963 -- 1331 26693 0.1858 0.2309 -- 94.0
X Ray Diffraction 2.7963 2.9235 -- 1444 26479 0.1859 0.222 -- 94.0
X Ray Diffraction 2.9235 3.0776 -- 1402 26199 0.1854 0.2183 -- 93.0
X Ray Diffraction 3.0776 3.2703 -- 1308 25354 0.1812 0.2165 -- 89.0
X Ray Diffraction 3.2703 3.5227 -- 1273 24780 0.1711 0.203 -- 88.0
X Ray Diffraction 3.5227 3.8769 -- 1534 26867 0.1516 0.177 -- 96.0
X Ray Diffraction 3.8769 4.4372 -- 1400 26320 0.1285 0.1475 -- 94.0
X Ray Diffraction 4.4372 5.5878 -- 1330 25098 0.1266 0.145 -- 89.0
X Ray Diffraction 5.5878 39.1952 -- 1408 26153 0.1712 0.1719 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.3211
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.128
f_plane_restr 0.004
f_chiral_restr 0.084
f_angle_d 1.18
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 58460
Nucleic Acid Atoms 0
Heterogen Atoms 300
Solvent Atoms 4520

Software

Computing
Computing Package Purpose
Blue Ice Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement