Lysozyme

This example illustrates data collection with the PlateMate configured on a Rigaku MicroMax-007 HF X-ray generator equipped with a AFC11-chi goniometer and a Saturn 944 HG CCD detector. A 120 µm lysozyme crystal, located in well E1 of a Greiner low-profile plate, was centered in the X-ray beam. 43° of data were then collected at room temperature using an exposure time of 20 seconds per 0.5°. The total collection time for the data set was 28 minutes, 40 seconds.




Lysozyme crystal used for data collection


Example of diffraction images obtained with an
exposure time of 20 seconds for 0.5°



Detector distance Δω Osc. range # img Exp time Total exposure time
80 mm 0.5° -33° < ω < 10° 86 20 sec 28 min 40 sec

Data collection parameters



Space group P43212
Unit cell a = 79.24 Å
c = 38.01 Å
Resolution 2.7 Å
Mosaicity 0.31 - 0.35°
Total reflections 11538
Unique reflections 3639
Rejected reflections 26 = 0.23%
Completeness 90.7% (79.5%)
Redundancy 3.5 (2.0)
I/σ(I) 13.9 (2.8)
Linear Rmerge9.0%
χ² 1.276 (0.723)

Crystal parameters and scaling statistics obtained in HKL-3000R
Numbers in () are for last shell.




Plots of χ² and R-factor vs. resolution.
Orange: χ² merged; Blue: χ² anomalous;
Green: R-factor merged; Red: R-factor anomalous


Plots of I/σ(I) vs. resolution.
Blue: I/σ(I) merged; Red: I/σ(I) anomalous


The lysozyme structure was solved using molecular replacement methods in HKL-3000R. HKL-3000R used the program MOLREP and PDB ID ‘1HEL’ as the starting model, from which ligands and waters were removed. Using data to 3.0 Å, MOLREP readily found a solution.

The model was then subjected to 5 cycles of rigid body refinement using REFMAC and data to 3.0 Å, followed by 10 cycles of restrained atomic refinement using data to 2.7 Å. The Rfac and Rfree values without the localized waters or correcting for bulk solvent contribution were 17.5% and 27.5%, respectively.



2Fo-Fc maps contoured at 1.5σ