7Q7P | pdb_00007q7p

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

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	60:40 monoolein with UQ2, protein 40 mg/mL concentration.

Crystal Properties
Matthews coefficient	Solvent content
3.62	65.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.9	α = 90
b = 125.3	β = 90
c = 182.7	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	CCD	MPCCD		2018-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.4	SACLA	BL2

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (All)	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	2.4	73.92	100	0.994	0.1057	7.87	7.05		76977

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	2.4	2.42			0.42

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	2I5N	2.4	73.92	73189	3808	100	0.167	0.1648	0.17	0.2044	0.21	49

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]
0.782			1.757		-2.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.859
r_dihedral_angle_4_deg	20.526
r_dihedral_angle_3_deg	16.288
r_lrange_it	7.782
r_lrange_other	7.782
r_dihedral_angle_1_deg	6.89
r_dihedral_angle_other_3_deg	6.571
r_scangle_it	5.679
r_scangle_other	5.678
r_mcangle_it	4.719
r_mcangle_other	4.719
r_scbond_it	3.589
r_scbond_other	3.589
r_mcbond_it	3.112
r_mcbond_other	3.11
r_angle_refined_deg	2.152
r_angle_other_deg	1.239
r_nbd_refined	0.195
r_nbd_other	0.194
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.092
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9270
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	912

Software

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