Experiment: 7KNK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	193L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	293	Rice vinegar, Common salt and Baking powder

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.483	α = 90
b = 78.483	β = 90
c = 37.104	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	MARMOSAIC 325 mm CCD	Rh coated collimating mirror, Toroidal focusing mirror	2020-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	1.195	SSRL	BL14-1

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	1.45	39.27	100	0.056	0.058	0.017	1	24.6	11.4		21165

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	1.45	1.47	99.9		1.325	1.416	0.487	0.682		8.2

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 (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	193l	1.45	39.27	20058	1059	99.97	0.16	0.1573	0.16	0.2131	0.22	RANDOM	20.431

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]
-0.57			-0.57		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.082
r_dihedral_angle_4_deg	17.738
r_dihedral_angle_3_deg	13.915
r_dihedral_angle_1_deg	6.682
r_rigid_bond_restr	2.573
r_angle_refined_deg	1.547
r_angle_other_deg	1.547
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.082
r_dihedral_angle_4_deg	17.738
r_dihedral_angle_3_deg	13.915
r_dihedral_angle_1_deg	6.682
r_rigid_bond_restr	2.573
r_angle_refined_deg	1.547
r_angle_other_deg	1.547
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1000
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	2

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.