Experiment: 6KKM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RBL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	289	8-10% 2-Methyl-2,4-pentanediol and 0.1 M MES 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 222.117	α = 90
b = 228.541	β = 90
c = 162.336	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 PILATUS3 S 6M		2018-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97892	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3	50	100	0.195	16	13.5		82605

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11			1.095

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	FREE R-VALUE	1RBL	3	49	69615	3725	88.51	0.2312	0.2287	0.23	0.2781	0.27	RANDOM	72.104

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]
-1.18			-1.04		2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.209
r_dihedral_angle_4_deg	15.666
r_dihedral_angle_3_deg	14.197
r_dihedral_angle_1_deg	6.641
r_angle_other_deg	3.751
r_angle_refined_deg	1.4
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.209
r_dihedral_angle_4_deg	15.666
r_dihedral_angle_3_deg	14.197
r_dihedral_angle_1_deg	6.641
r_angle_other_deg	3.751
r_angle_refined_deg	1.4
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24810
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
HKL-2000	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.