X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 294.0
Details 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 5% (v/v) 2-Propanol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.98 α = 90
b = 102.95 β = 90
c = 234.43 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 -- 2012-04-27
Diffraction Radiation
Monochromator Protocol
Double silicon(111) crystal 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
2.1 50 87.9 0.091 -- -- 10.5 -- 113134 -- -- 23.77
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)
2.1 2.14 78.8 0.92 -- 2.5 10.5 --

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 2.094 47.131 -- 1.34 -- 107240 5358 83.33 -- 0.1501 0.1473 0.2044 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 2.0937 2.1175 -- 86 1762 0.1488 0.2112 -- 44.0
X Ray Diffraction 2.1175 2.1424 -- 128 2118 0.1472 0.2382 -- 52.0
X Ray Diffraction 2.1424 2.1685 -- 130 2408 0.1523 0.2131 -- 60.0
X Ray Diffraction 2.1685 2.196 -- 144 2526 0.1537 0.2514 -- 63.0
X Ray Diffraction 2.196 2.2249 -- 140 2773 0.1569 0.262 -- 69.0
X Ray Diffraction 2.2249 2.2553 -- 139 2817 0.1544 0.2179 -- 70.0
X Ray Diffraction 2.2553 2.2876 -- 164 2944 0.1606 0.2324 -- 73.0
X Ray Diffraction 2.2876 2.3217 -- 143 3029 0.1532 0.2351 -- 74.0
X Ray Diffraction 2.3217 2.358 -- 160 3092 0.159 0.2096 -- 77.0
X Ray Diffraction 2.358 2.3966 -- 166 3182 0.1574 0.2454 -- 79.0
X Ray Diffraction 2.3966 2.438 -- 166 3220 0.1499 0.27 -- 79.0
X Ray Diffraction 2.438 2.4823 -- 177 3211 0.1478 0.2309 -- 80.0
X Ray Diffraction 2.4823 2.53 -- 174 3258 0.1574 0.2176 -- 81.0
X Ray Diffraction 2.53 2.5817 -- 182 3336 0.1598 0.1985 -- 82.0
X Ray Diffraction 2.5817 2.6378 -- 160 3400 0.1611 0.227 -- 83.0
X Ray Diffraction 2.6378 2.6992 -- 201 3378 0.164 0.2578 -- 85.0
X Ray Diffraction 2.6992 2.7666 -- 169 3518 0.1633 0.2273 -- 86.0
X Ray Diffraction 2.7666 2.8414 -- 198 3582 0.1599 0.23 -- 88.0
X Ray Diffraction 2.8414 2.925 -- 181 3735 0.1575 0.2249 -- 91.0
X Ray Diffraction 2.925 3.0194 -- 212 3755 0.1608 0.2024 -- 93.0
X Ray Diffraction 3.0194 3.1273 -- 215 3909 0.1587 0.2307 -- 96.0
X Ray Diffraction 3.1273 3.2525 -- 205 3985 0.1622 0.1998 -- 98.0
X Ray Diffraction 3.2525 3.4005 -- 206 4013 0.146 0.1913 -- 98.0
X Ray Diffraction 3.4005 3.5797 -- 226 4010 0.1461 0.1886 -- 98.0
X Ray Diffraction 3.5797 3.8039 -- 254 4020 0.1383 0.1937 -- 99.0
X Ray Diffraction 3.8039 4.0975 -- 198 4088 0.126 0.1657 -- 99.0
X Ray Diffraction 4.0975 4.5095 -- 180 4146 0.1156 0.1644 -- 99.0
X Ray Diffraction 4.5095 5.1614 -- 209 4116 0.1187 0.1573 -- 99.0
X Ray Diffraction 5.1614 6.5001 -- 207 4205 0.156 0.21 -- 99.0
X Ray Diffraction 6.5001 47.1425 -- 238 4346 0.1625 0.2095 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.849
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.208
f_plane_restr 0.007
f_chiral_restr 0.078
f_angle_d 1.349
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16810
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 867

Software

Computing
Computing Package Purpose
CBASS Data Collection
DENZO 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
pdb_extract version: 3.11 data extraction
phenix refinement
DENZO data collection