Experiment: 2NVK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	200 mM Succinate, 22% PEG 6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.487	α = 90
b = 151.487	β = 90
c = 134.259	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	104	IMAGE PLATE	MAR scanner 345 mm plate	Xenocs FOX-2D Multilayer Mirrors	2006-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	15	98.7	0.059	13.2	7.85		22987

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	90.3		0.422	2.78		2075

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1H6V	2.4	15	21869	2201	93.84	0.203	0.198	0.247	RANDOM	49.14

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]
1.7	0.85		1.7		-2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.685
r_dihedral_angle_4_deg	19.865
r_dihedral_angle_3_deg	18.707
r_dihedral_angle_1_deg	6.15
r_scangle_it	1.836
r_angle_refined_deg	1.359
r_scbond_it	1.12
r_mcangle_it	0.761
r_mcbond_it	0.425
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.685
r_dihedral_angle_4_deg	19.865
r_dihedral_angle_3_deg	18.707
r_dihedral_angle_1_deg	6.15
r_scangle_it	1.836
r_angle_refined_deg	1.359
r_scbond_it	1.12
r_mcangle_it	0.761
r_mcbond_it	0.425
r_nbtor_refined	0.304
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.2
r_symmetry_hbond_refined	0.197
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3670
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	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.