X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 277.0
Details 18.5% PEG2000, 100 mM sodium tartrate, 50 mM ADA, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.37 α = 90
b = 107.61 β = 99.83
c = 79.11 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-01-31
Diffraction Radiation
Monochromator Protocol
diamond(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.12712 APS 21-ID-D

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
1.89 77.95 95.9 -- 0.058 -- 3.5 67072 64297 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)
1.89 1.97 89.8 -- 0.309 5.2 3.0 --

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 1.894 38.973 -- 1.34 64297 63974 3188 95.04 -- 0.1798 0.1777 0.219 --
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 1.894 1.9219 -- 106 1972 0.4536 0.4852 -- 71.0
X Ray Diffraction 1.9219 1.952 -- 149 2634 0.2751 0.3606 -- 96.0
X Ray Diffraction 1.952 1.984 -- 151 2708 0.2127 0.2978 -- 98.0
X Ray Diffraction 1.984 2.0182 -- 129 2708 0.1966 0.2727 -- 98.0
X Ray Diffraction 2.0182 2.0549 -- 159 2747 0.1891 0.2624 -- 98.0
X Ray Diffraction 2.0549 2.0944 -- 142 2665 0.184 0.2313 -- 98.0
X Ray Diffraction 2.0944 2.1371 -- 134 2745 0.1771 0.2391 -- 98.0
X Ray Diffraction 2.1371 2.1836 -- 148 2698 0.1817 0.226 -- 98.0
X Ray Diffraction 2.1836 2.2344 -- 110 2365 0.2292 0.2457 -- 84.0
X Ray Diffraction 2.2344 2.2903 -- 116 2104 0.2338 0.3102 -- 76.0
X Ray Diffraction 2.2903 2.3522 -- 142 2732 0.1863 0.2115 -- 99.0
X Ray Diffraction 2.3522 2.4214 -- 143 2740 0.1756 0.253 -- 98.0
X Ray Diffraction 2.4214 2.4995 -- 139 2722 0.1821 0.2024 -- 99.0
X Ray Diffraction 2.4995 2.5888 -- 137 2765 0.1799 0.2447 -- 98.0
X Ray Diffraction 2.5888 2.6925 -- 140 2746 0.187 0.2481 -- 99.0
X Ray Diffraction 2.6925 2.815 -- 170 2721 0.1828 0.2371 -- 99.0
X Ray Diffraction 2.815 2.9633 -- 145 2720 0.1857 0.2138 -- 99.0
X Ray Diffraction 2.9633 3.1489 -- 136 2771 0.1844 0.2405 -- 99.0
X Ray Diffraction 3.1489 3.3919 -- 147 2737 0.1747 0.2274 -- 99.0
X Ray Diffraction 3.3919 3.733 -- 129 2704 0.1636 0.1947 -- 96.0
X Ray Diffraction 3.733 4.2726 -- 140 2659 0.1435 0.1759 -- 95.0
X Ray Diffraction 4.2726 5.3808 -- 141 2710 0.1356 0.1621 -- 97.0
X Ray Diffraction 5.3808 38.9814 -- 135 2713 0.1531 0.16 -- 95.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.085
f_dihedral_angle_d 13.193
f_angle_d 1.233
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6634
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 400

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
PHASER model building
HKL-2000 data collection