Experiment: 3GNK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L4J	PDB entry 1L4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	CaCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K, temperature 290.0K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.97	α = 90
b = 24.17	β = 110.37
c = 73.89	γ = 90

Symmetry
Space Group	C 1 2 1

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	OXFORD SAPPHIRE CCD	multilayer optics		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.5418

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	2.1	16.347	99.41	0.062	11.44	3.9	6643	6622	1	1	17.122

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)
	2.1	2.155	99.41		0.194	2.35	3	1773

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 1L4J	2.1	16.347	6622	6622	311	99.41	0.218	0.218	0.214	0.21	0.306	0.3	RANDOM	17.122

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]
-1.24		0.06	1.3		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.285
r_scangle_it	1.079
r_scbond_it	0.716
r_nbtor_refined	0.293
POTENTIAL METAL-ION REFINED ATOMS (A)	0.163
r_nbd_refined	0.162
r_xyhbond_nbd_refined	0.119
r_symmetry_vdw_refined	0.098
r_symmetry_hbond_refined	0.071
r_chiral_restr	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.285
r_scangle_it	1.079
r_scbond_it	0.716
r_nbtor_refined	0.293
POTENTIAL METAL-ION REFINED ATOMS (A)	0.163
r_nbd_refined	0.162
r_xyhbond_nbd_refined	0.119
r_symmetry_vdw_refined	0.098
r_symmetry_hbond_refined	0.071
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	808
Solvent Atoms	183
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction
MOLREP	phasing
REFMAC	refinement

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.