7CKV | pdb_00007ckv

Crystal structure of Cyanobacteriochrome GAF domain in Pr state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VV4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	27% PEG 4000, 0.2M MgCl2, 0.1M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.73	α = 90
b = 101.334	β = 91.788
c = 41.81	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270		2020-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AichiSR BEAMLINE BL2S1	1.12	AichiSR	BL2S1

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	1.63	41.79	99.6	0.046	0.054	0.027	0.996	13.3	3.9		36876			15

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	1.63	1.66	99.9		0.483	0.562	0.285	0.837	2.2	3.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3vv4	1.63	38.663	36846	1753	99.525	0.16	0.1583	0.17	0.1991	0.21	Random selection	20.225

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]
1.14		-0.669	-0.822		-0.275

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.052
r_dihedral_angle_4_deg	19.451
r_dihedral_angle_3_deg	13.173
r_dihedral_angle_other_3_deg	7.966
r_dihedral_angle_1_deg	6.629
r_lrange_it	6.578
r_lrange_other	6.46
r_scangle_it	4.444
r_scangle_other	4.443
r_scbond_other	2.892
r_scbond_it	2.891
r_mcangle_other	2.771
r_mcangle_it	2.767
r_mcbond_it	1.893
r_mcbond_other	1.885
r_angle_refined_deg	1.718
r_angle_other_deg	1.468
r_symmetry_nbd_refined	0.324
r_nbd_refined	0.224
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.182
r_nbd_other	0.18
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.17
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2273
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	87

Software

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