X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 1.9 M ammonium sulfate, 5% w/v PEG400, 0.1 M MES-NaOH, 20% v/v glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.22 α = 90
b = 123.22 β = 90
c = 68.82 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2004-08-20
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 -- EMBL/DESY, HAMBURG X31

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
1.86 38.97 99.6 0.12 -- -- 7.2 44717 44717 -- -- --
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)
1.86 1.96 95.8 0.39 -- 3.5 7.0 --

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 1.861 38.967 -- 1.37 42465 44717 2254 99.6 -- 0.18 0.1782 0.2137 --
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 1.8613 1.9018 -- 148 2432 0.2723 0.2842 -- 94.0
X Ray Diffraction 1.9018 1.946 -- 136 2608 0.1987 0.2266 -- 100.0
X Ray Diffraction 1.946 1.9947 -- 141 2618 0.1867 0.2311 -- 100.0
X Ray Diffraction 1.9947 2.0486 -- 140 2642 0.1735 0.2255 -- 100.0
X Ray Diffraction 2.0486 2.1089 -- 144 2617 0.1633 0.1983 -- 100.0
X Ray Diffraction 2.1089 2.177 -- 126 2651 0.1646 0.1948 -- 100.0
X Ray Diffraction 2.177 2.2548 -- 154 2603 0.1703 0.2085 -- 100.0
X Ray Diffraction 2.2548 2.345 -- 127 2652 0.1709 0.222 -- 100.0
X Ray Diffraction 2.345 2.4517 -- 144 2655 0.1679 0.2123 -- 100.0
X Ray Diffraction 2.4517 2.581 -- 155 2631 0.176 0.2249 -- 100.0
X Ray Diffraction 2.581 2.7426 -- 146 2657 0.1777 0.2544 -- 100.0
X Ray Diffraction 2.7426 2.9543 -- 135 2672 0.1892 0.1929 -- 100.0
X Ray Diffraction 2.9543 3.2515 -- 140 2688 0.1817 0.2112 -- 100.0
X Ray Diffraction 3.2515 3.7217 -- 130 2709 0.1727 0.2019 -- 100.0
X Ray Diffraction 3.7217 4.6877 -- 142 2738 0.1516 0.1839 -- 100.0
X Ray Diffraction 4.6877 38.9754 -- 146 2890 0.2014 0.2271 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.1285
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.1285
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.257
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_angle_d 1.072
f_chiral_restr 0.072
f_plane_restr 0.004
f_dihedral_angle_d 19.342
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3272
Nucleic Acid Atoms 0
Heterogen Atoms 159
Solvent Atoms 328

Software

Software
Software Name Purpose
PHENIX refinement version: 1.6.4_486
AMoRE phasing
REFMAC refinement version: 5.5.0066
MOSFLM data reduction
SCALA data scaling
MAR345dtb data collection