11YO | pdb_000011yo

Single-conformation model re-refinement of 2F/S3-rich PSII intermediate structure at 2.09 Angstrom resolution

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	6W1V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		298	0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.958	α = 90
b = 221.646	β = 90
c = 307.786	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	RAYONIX MX340-HS		2019-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE MFX	1.30192	SLAC LCLS	MFX

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)	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	2.09	33.65	99.8	0.99	12.8	81		468019

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	2.09	2.13			0.05

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.09	33.65	466446	4162	99.837	0.1841	0.1835	0.1948	0.2433	0.2495	40.956

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]
-1.49			-0.068		1.557

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.63
r_dihedral_angle_6_deg	16.676
r_dihedral_angle_3_deg	14.9
r_lrange_other	7.704
r_lrange_it	7.703
r_scangle_it	7.397
r_scangle_other	7.397
r_dihedral_angle_1_deg	6.817
r_scbond_it	6.228
r_scbond_other	6.228
r_mcangle_it	5.903
r_mcangle_other	5.903
r_angle_refined_deg	5.191
r_mcbond_it	5.107
r_mcbond_other	5.106
r_angle_other_deg	1.215
r_chiral_restr	0.684
r_symmetry_nbd_refined	0.363
r_symmetry_xyhbond_nbd_refined	0.301
r_nbd_other	0.258
r_nbd_refined	0.242
r_symmetry_nbd_other	0.229
r_xyhbond_nbd_refined	0.205
r_nbtor_refined	0.203
r_symmetry_xyhbond_nbd_other	0.129
r_symmetry_nbtor_other	0.098
r_gen_planes_other	0.04
r_bond_refined_d	0.027
r_metal_ion_refined	0.027
r_gen_planes_refined	0.021
r_dihedral_angle_other_2_deg	0.018
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	41594
Nucleic Acid Atoms
Solvent Atoms	1994
Heterogen Atoms	8608

Software

Software
Software Name	Purpose
REFMAC	refinement
cctbx.xfel	data reduction
cxi.merge	data scaling
PHASER	phasing