X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 298.0
Details 26-33% PEG8000, 0.1 M Tris, pH 8.0, 2 mM zinc sulfate, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.61 α = 90
b = 74.61 β = 90
c = 49.74 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2006-06-15
Diffraction Radiation
Monochromator Protocol
sagitally focused Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.9099 SLS X06SA

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
1.5 33.37 99.9 0.077 -- -- 6.04 -- 43872 1.0 1.0 --
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)
1.5 1.55 100.0 0.467 -- 3.0 5.98 4385

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
FOURIER SYNTHESIS 1.5 33.369 -- 1.35 -- 43869 2152 99.75 -- 0.1816 0.1805 0.2007 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 1.5 1.5171 -- 146 2776 0.3245 0.2969 -- 100.0
X Ray Diffraction 1.5171 1.5349 -- 136 2643 0.2799 0.3106 -- 100.0
X Ray Diffraction 1.5349 1.5536 -- 150 2767 0.2806 0.282 -- 100.0
X Ray Diffraction 1.5536 1.5733 -- 152 2709 0.2629 0.2916 -- 100.0
X Ray Diffraction 1.5733 1.594 -- 136 2696 0.2515 0.2451 -- 100.0
X Ray Diffraction 1.594 1.6158 -- 140 2687 0.2429 0.2533 -- 100.0
X Ray Diffraction 1.6158 1.6389 -- 148 2708 0.2209 0.2461 -- 100.0
X Ray Diffraction 1.6389 1.6634 -- 152 2745 0.2251 0.2419 -- 100.0
X Ray Diffraction 1.6634 1.6894 -- 168 2703 0.2224 0.2593 -- 100.0
X Ray Diffraction 1.6894 1.7171 -- 136 2719 0.2089 0.2481 -- 100.0
X Ray Diffraction 1.7171 1.7467 -- 178 2706 0.2014 0.2663 -- 100.0
X Ray Diffraction 1.7467 1.7784 -- 134 2723 0.2021 0.2528 -- 100.0
X Ray Diffraction 1.7784 1.8126 -- 164 2619 0.184 0.2019 -- 100.0
X Ray Diffraction 1.8126 1.8496 -- 128 2750 0.1816 0.2102 -- 100.0
X Ray Diffraction 1.8496 1.8899 -- 152 2667 0.1824 0.2628 -- 100.0
X Ray Diffraction 1.8899 1.9338 -- 143 2749 0.1873 0.2013 -- 100.0
X Ray Diffraction 1.9338 1.9822 -- 115 2789 0.178 0.2297 -- 100.0
X Ray Diffraction 1.9822 2.0358 -- 120 2693 0.1713 0.1935 -- 100.0
X Ray Diffraction 2.0358 2.0957 -- 148 2707 0.168 0.1823 -- 100.0
X Ray Diffraction 2.0957 2.1633 -- 97 2749 0.1707 0.1692 -- 99.0
X Ray Diffraction 2.1633 2.2406 -- 141 2731 0.1789 0.1844 -- 100.0
X Ray Diffraction 2.2406 2.3303 -- 138 2690 0.1684 0.1987 -- 100.0
X Ray Diffraction 2.3303 2.4363 -- 133 2708 0.1744 0.192 -- 99.0
X Ray Diffraction 2.4363 2.5647 -- 154 2707 0.1717 0.1998 -- 100.0
X Ray Diffraction 2.5647 2.7253 -- 135 2716 0.1779 0.1787 -- 100.0
X Ray Diffraction 2.7253 2.9356 -- 141 2729 0.1809 0.2151 -- 100.0
X Ray Diffraction 2.9356 3.2308 -- 138 2704 0.1757 0.1702 -- 100.0
X Ray Diffraction 3.2308 3.6978 -- 156 2712 0.1557 0.1937 -- 100.0
X Ray Diffraction 3.6978 4.6569 -- 144 2732 0.1446 0.1502 -- 100.0
X Ray Diffraction 4.6569 33.377 -- 161 2683 0.1802 0.1934 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.4166
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_chiral_restr 0.082
f_plane_restr 0.005
f_angle_d 1.114
f_dihedral_angle_d 12.486
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1699
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 338

Software

Software
Software Name Purpose
d*TREK data reduction version: 9.9.9.4L
PHENIX refinement version: 1.8_1069
PDB_EXTRACT data extraction version: 3.11
d*TREK data scaling
CNX phasing