8WVE | pdb_00008wve

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	313	sodium/pottasium tartrae, sodium acetate, KCl

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.188	α = 90
b = 94.188	β = 90
c = 179.168	γ = 120

Symmetry
Space Group	P 63

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 16M		2020-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.729	47.4	99.8	0.998	14.9	10.7		23865

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.729	2.73			0.998		11

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 (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	THROUGHOUT	2.729	47.138	23864	1109	99.695	0.283	0.28	0.28	0.338	0.33	RANDOM	61.884

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]
-5.822	-2.911		-5.822		18.886

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.988
r_dihedral_angle_6_deg	12.844
r_lrange_it	4.996
r_lrange_other	4.995
r_dihedral_angle_2_deg	3.303
r_dihedral_angle_1_deg	3.29
r_mcangle_other	2.863
r_mcangle_it	2.862
r_scangle_it	2.182
r_scangle_other	2.181
r_mcbond_it	1.632
r_mcbond_other	1.63
r_scbond_it	1.201
r_scbond_other	1.201
r_angle_refined_deg	0.668
r_dihedral_angle_other_2_deg	0.535
r_symmetry_xyhbond_nbd_refined	0.288
r_angle_other_deg	0.272
r_symmetry_nbd_other	0.211
r_symmetry_nbd_refined	0.207
r_nbd_other	0.203
r_nbd_refined	0.188
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.16
r_metal_ion_refined	0.134
r_symmetry_xyhbond_nbd_other	0.089
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.029
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6407
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	128

Software

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