8K9O | pdb_00008k9o

Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CKV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PEG 8000, magnesium acetate, sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.273	α = 90
b = 64.273	β = 90
c = 84.116	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM 270		2022-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AichiSR BEAMLINE BL2S1	1.1211	AichiSR	BL2S1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	45.489	100	0.069	1	26.2	13.9		18446			19.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	100		0.903	0.876	3.4	14.1

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	7CKV	1.75	45.489	18395	861	99.962	0.19	0.1875	0.2	0.2311	0.24	24.374

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]
0.274			0.274		-0.547

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.28
r_dihedral_angle_4_deg	14.631
r_dihedral_angle_3_deg	14.373
r_dihedral_angle_1_deg	7.094
r_lrange_it	6.26
r_lrange_other	6.24
r_scangle_it	5.027
r_scangle_other	5.025
r_scbond_it	3.285
r_scbond_other	3.285
r_mcangle_it	2.948
r_mcangle_other	2.948
r_mcbond_it	2.195
r_mcbond_other	2.187
r_angle_refined_deg	1.706
r_angle_other_deg	1.449
r_symmetry_nbd_refined	0.221
r_nbd_refined	0.211
r_symmetry_nbd_other	0.183
r_nbd_other	0.179
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.122
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1438
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	43

Software

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