7Q7Q | pdb_00007q7q

LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE

X-RAY DIFFRACTION

---

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NJ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	This LCP crystallization was performed in wells with 200uL precipitant and 20uL LCP+protein.

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.66	α = 90
b = 125.13	β = 90
c = 182.38	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	PSI JUNGFRAU 16M		2019-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SwissFEL ARAMIS BEAMLINE ESA	1.102	SwissFEL ARAMIS	ESA

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	160275	260392	160275

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1		0.047 (µl/min)	undefined (µm)

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	2.25	23.702	100	0.995	9.6	11.888		92545

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	2.25	2.27			0.54

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5NJ4	2.25	23.702	92515	4602	99.856	0.169	0.1678	0.18	0.2028	0.21	48.98

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]
0.613			1.99		-2.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.062
r_dihedral_angle_4_deg	19.753
r_dihedral_angle_other_3_deg	16.304
r_dihedral_angle_3_deg	15.84
r_lrange_it	7.358
r_lrange_other	7.358
r_dihedral_angle_1_deg	6.581
r_scangle_it	5.594
r_scangle_other	5.594
r_mcangle_it	4.372
r_mcangle_other	4.372
r_scbond_it	3.515
r_scbond_other	3.514
r_mcbond_it	2.873
r_mcbond_other	2.871
r_angle_refined_deg	2.13
r_angle_other_deg	1.203
r_nbd_refined	0.195
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.168
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.098
r_symmetry_xyhbond_nbd_other	0.086
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_refined	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9263
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	1022

Software

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