X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 289.0
Details 14% peg8000, 0.1 M Tris. 1.2 M NaCl, 125mM KCl, 150mM Arg-HCl,20mM MgCl2, 5% glycerol, pH 7.5, VAPOR DIFFUSION, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.62 α = 90
b = 127.62 β = 90
c = 73.99 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2012-06-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.0 APS 19-ID

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 99.8 0.062 0.053 -- 9.5 36479 36412 2.0 2.0 --
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 2.14 100.0 0.71 0.646 3.0 9.7 --

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 2.1 40.357 -- 1.34 36527 36359 2000 99.54 -- 0.2006 0.199 0.2276 --
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 2.0938 2.1462 -- 135 2321 0.2252 0.2849 -- 96.0
X Ray Diffraction 2.1462 2.2042 -- 141 2435 0.2065 0.2506 -- 100.0
X Ray Diffraction 2.2042 2.269 -- 142 2424 0.2038 0.2395 -- 100.0
X Ray Diffraction 2.269 2.3423 -- 140 2406 0.1886 0.2162 -- 100.0
X Ray Diffraction 2.3423 2.426 -- 140 2419 0.1845 0.1935 -- 100.0
X Ray Diffraction 2.426 2.5231 -- 142 2439 0.1862 0.237 -- 100.0
X Ray Diffraction 2.5231 2.6379 -- 144 2465 0.1951 0.2416 -- 100.0
X Ray Diffraction 2.6379 2.777 -- 142 2449 0.1981 0.2197 -- 100.0
X Ray Diffraction 2.777 2.9509 -- 143 2454 0.2114 0.2472 -- 100.0
X Ray Diffraction 2.9509 3.1786 -- 142 2436 0.2102 0.2436 -- 100.0
X Ray Diffraction 3.1786 3.4984 -- 144 2483 0.2022 0.2317 -- 100.0
X Ray Diffraction 3.4984 4.0042 -- 146 2492 0.1983 0.2176 -- 100.0
X Ray Diffraction 4.0042 5.0433 -- 146 2522 0.1725 0.1918 -- 100.0
X Ray Diffraction 5.0433 40.3641 -- 153 2614 0.2194 0.2534 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.5214
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.5214
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.0428
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.071
f_dihedral_angle_d 14.55
f_angle_d 1.098
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2449
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 101

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.1_743) Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
PHENIX version: (phenix.refine: 1.7.1_743) model building
HKL-3000 data collection