7CLJ | pdb_00007clj

Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	5	293	25% PEG 350 MME, 100mM Na-citrate, 100mM ammonium sulfate or lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.86	α = 90
b = 72.86	β = 90
c = 115.05	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	100	PIXEL	DECTRIS EIGER X 9M		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.000	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.6	30	99.1	0.38	0.982	5.36	7.71		9975

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.76	98.6		1.806	0.484	1.04	7.6

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	6is6	2.6	28.368	9975	502	99.096	0.225	0.2215	0.23	0.2834	0.29	36.753

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]
-0.017			-0.017		0.033

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.561
r_dihedral_angle_3_deg	18.287
r_dihedral_angle_4_deg	15.758
r_lrange_it	6.992
r_lrange_other	6.991
r_dihedral_angle_1_deg	5.284
r_scangle_it	3.25
r_scangle_other	3.249
r_mcangle_it	3.158
r_mcangle_other	3.156
r_scbond_it	1.988
r_scbond_other	1.987
r_mcbond_other	1.885
r_mcbond_it	1.884
r_angle_refined_deg	1.359
r_angle_other_deg	1.166
r_symmetry_xyhbond_nbd_refined	0.435
r_symmetry_nbd_refined	0.249
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.174
r_nbd_other	0.173
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2007
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	250

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing