Table 2. Processing outcome on measured XFEL still shots from thermolysin.

	Previous work†	Equation (1) only	Equations (1) and (2)	Best practice
Protocol	NM	4	5	6
Refinement target
Initial triclinic cell	Equation (1)	Equation (1)	Equation (2)	Equation (2)
Constrained hexagonal cell	Equation (2)	Equation (1)	Equation (1)	Equation (2)
Fitting of mosaicity and block size	Least squares	Maximum likelihood	Maximum likelihood	Maximum likelihood
Indexing results‡
Total No. of hits with >15 Bragg spots	14041	14041	14041	14041
No. of integrated and merged lattices	11151	12097	11958	12551
Model accuracy
Half-width mosaicity ()	0.471	0.292	0.286	0.168
Mosaic block size ()	2920	4320	4320	4220
Integrated data results
Individual image CC (%)	32.5	32.0	32.3	40.2
No. of measurements, 512.2	5793963	6605566	6538120	5036076
Positive measurements, 512.2	3893827	4297065	4265829	3626262
Negative measurements (%)	33	35	35	28
Structure-factor merging
Unique Miller indices, 512.2	17156	17198	17193	17297
Multiplicity of observation	222	245	243	207
Completeness (%)	97.9	98.2	98.2	98.8
I/(I)	41.1	36.1	36.7	56.7
CCiso versus 4ow3 (based on intensities) (%)	90.1	86.8	86.6	94.7
R iso versus 4ow3 (based on intensities) (%)	22.5	23.6	23.4	18.0
Structure-factor quality tests
|L| (acentric theoretical = 0.5)	0.340	0.302	0.304	0.376
L 2 (acentric theoretical = 0.333)	0.169	0.137	0.138	0.202
P(Z) maximum deviation (acentric)	0.159	0.201	0.196	0.121
P(Z) maximum deviation (centric)	0.238	0.271	0.265	0.198
Quality of refined structure
R work (%)	21.9	24.5	24.2	20.6%
R free (%)	27.9	29.6	29.8	26.0
Zn2+ anomalous difference map peak height ()	3.5	2.9	3.0	5.9

^†This column replicates the method in our previous publication (Hattne et al., 2014 ▶) used to derive the thermolysin structure (PDB entry 4ow3).

^‡For the thermolysin data analysis, candidate Bragg spots were chosen with a minimum spot area of two square pixels.