8R96 | pdb_00008r96

Crystal structure of the cryorhodopsin CryoR2 at pH 4.6, type A crystals

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	4.6	293	1.2M Na/K-Pi pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.565	α = 90
b = 295.665	β = 90
c = 185.5	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER2 X 16M		2023-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.976	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.457	92.75	65.6	0.064	0.9964	8.493	13.44		56393

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.457	2.719			0.962	0.304

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.46	20	53453	2746	65.39	0.23952	0.23874	0.2462	0.25445	0.2633	RANDOM	57.574

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]
0.72			-1.1		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.46
r_dihedral_angle_4_deg	15.642
r_dihedral_angle_3_deg	12.734
r_long_range_B_refined	10.238
r_long_range_B_other	10.238
r_mcangle_it	7.408
r_mcangle_other	7.408
r_scangle_other	7.324
r_scbond_other	4.758
r_scbond_it	4.734
r_mcbond_it	4.72
r_mcbond_other	4.719
r_dihedral_angle_1_deg	4.534
r_angle_other_deg	1.067
r_angle_refined_deg	1.062
r_chiral_restr	0.026
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10838
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	175

Software

Software
Software Name	Purpose
REFMAC	refinement
STARANISO	data scaling
MOLREP	phasing
XDS	data reduction