X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 293.0
Details 1.1 M sodium malonate, 0.1 HEPES, 0.5% (v/v) Jeffamine ED-2001, pH 7.0, vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.07 α = 90
b = 75.07 β = 90
c = 129.26 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
pixel DECTRIS PILATUS 6M -- 2012-02-25
Diffraction Radiation
Monochromator Protocol
-- Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-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
1.6 65.01 100.0 0.076 -- -- 10.2 54313 54313 0.0 -3.0 --
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)
1.6 1.63 100.0 0.01257 -- 2.1 10.3 2687

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 1.6 37.535 -- 1.72 -- 54268 2761 99.99 -- 0.1626 0.1611 0.1901 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 1.6 1.6276 -- 141 2554 0.2386 0.2552 -- 100.0
X Ray Diffraction 1.6276 1.6572 -- 128 2583 0.2271 0.2772 -- 100.0
X Ray Diffraction 1.6572 1.6891 -- 150 2521 0.2295 0.2443 -- 100.0
X Ray Diffraction 1.6891 1.7235 -- 119 2611 0.2168 0.2367 -- 100.0
X Ray Diffraction 1.7235 1.761 -- 149 2550 0.2002 0.237 -- 100.0
X Ray Diffraction 1.761 1.802 -- 161 2553 0.2001 0.2176 -- 100.0
X Ray Diffraction 1.802 1.8471 -- 140 2567 0.1771 0.2 -- 100.0
X Ray Diffraction 1.8471 1.897 -- 144 2549 0.164 0.2109 -- 100.0
X Ray Diffraction 1.897 1.9528 -- 141 2571 0.1638 0.1893 -- 100.0
X Ray Diffraction 1.9528 2.0158 -- 142 2569 0.1608 0.2143 -- 100.0
X Ray Diffraction 2.0158 2.0879 -- 134 2593 0.1534 0.179 -- 100.0
X Ray Diffraction 2.0879 2.1715 -- 132 2561 0.1484 0.1788 -- 100.0
X Ray Diffraction 2.1715 2.2703 -- 145 2588 0.142 0.1714 -- 100.0
X Ray Diffraction 2.2703 2.39 -- 140 2563 0.1453 0.153 -- 100.0
X Ray Diffraction 2.39 2.5397 -- 123 2593 0.1529 0.1789 -- 100.0
X Ray Diffraction 2.5397 2.7357 -- 143 2567 0.1587 0.1874 -- 100.0
X Ray Diffraction 2.7357 3.0109 -- 144 2590 0.1713 0.1923 -- 100.0
X Ray Diffraction 3.0109 3.4463 -- 130 2579 0.1649 0.1974 -- 100.0
X Ray Diffraction 3.4463 4.341 -- 124 2611 0.1409 0.155 -- 100.0
X Ray Diffraction 4.341 37.5458 -- 131 2634 0.1581 0.2054 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.8953
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.926
f_plane_restr 0.008
f_chiral_restr 0.083
f_angle_d 1.046
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2703
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 259

Software

Computing
Computing Package Purpose
JDIRECTOR Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1148) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 0.1.27 data reduction