6PGK

Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at 2.9 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	6.4	283	0-3 mM MgSO4 5 mM MES 0.02 % beta-DDM

Crystal Properties
Matthews coefficient	Solvent content
	79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 279.1	α = 90
b = 164.6	β = 119.25
c = 284.1	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	AGIPD		2017-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	EUROPEAN XFEL BEAMLINE SPB/SFX	1.399	European XFEL	SPB/SFX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.9	39.88	99.4	0.92	3.5	94		493312			61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	93.9		0.023	0.47	52

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JB0	2.9	39.88	467105	24635	99.26	0.3	0.29809	0.3	0.33596	0.34	RANDOM	55.964

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.78		0.36	-1.37		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.143
r_dihedral_angle_3_deg	17.758
r_dihedral_angle_4_deg	17.209
r_dihedral_angle_1_deg	7.131
r_long_range_B_refined	5.374
r_long_range_B_other	5.374
r_mcangle_it	4.453
r_mcangle_other	4.453
r_scangle_other	3.384
r_mcbond_it	2.709
r_mcbond_other	2.709
r_angle_refined_deg	2.21
r_scbond_it	2.07
r_scbond_other	2.07
r_angle_other_deg	1.535
r_chiral_restr	0.095
r_gen_planes_other	0.012
r_gen_planes_refined	0.01
r_bond_refined_d	0.006
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	52485
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	19976

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing