7Q7H | pdb_00007q7h

Room temperature structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H mutant at 51 MPa helium gas pressure in a sapphire capillary

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		289	20-25 mg/ml protein solution was mixed 1:1 with lipid sponge phase. The mixture was filled into a sealed plastic tip covered with an excess amount of 1 M trisodium citrate and incubated in the dark at 289 K for 1 week.

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.29	α = 90
b = 102.29	β = 90
c = 237.99	γ = 90

Symmetry
Space Group	P 42 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	295	PIXEL	DECTRIS PILATUS3 X CdTe 2M		2019-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.477	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.49	46.99	98.85	0.306	0.326	0.109	0.984	5.86	8.4		44663			40.43

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.579	99.18		2.105	2.266	0.818	0.347	1.01	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3V3Y	2.49	46.99	1.33	44643	1794	98.87	0.1782	0.1768	0.18	0.212	0.21	51.03

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.8974
f_angle_d	0.562
f_chiral_restr	0.0386
f_plane_restr	0.0034
f_bond_d	0.0027

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6466
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	689

Software

Software
Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.