Experiment: 5M35

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NKX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277.15	0.17 M Ammonium acetate; 0.085 M Sodium citrate pH 5.6; 25.5%(w/v) PEG 4000; 15%(v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.221	α = 90
b = 104.075	β = 90
c = 114.451	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS 6M		2015-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99983	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.38	44.85	99.7	0.066	0.999	16.76	6.4		35499		-3	58.906

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.5	99.9		0.598	0.757	3.11

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	3NKX	2.38	44.85	33123	1746	100	0.2271	0.2243	0.24	0.2772	0.27	RANDOM	55.997

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]
-0.44			3.6		-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.41
r_dihedral_angle_3_deg	21.123
r_dihedral_angle_4_deg	15.705
r_dihedral_angle_1_deg	15.346
r_scangle_it	5.159
r_scbond_it	3.189
r_mcangle_it	2.14
r_angle_refined_deg	1.9
r_mcbond_it	1.111
r_angle_other_deg	1.034

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.41
r_dihedral_angle_3_deg	21.123
r_dihedral_angle_4_deg	15.705
r_dihedral_angle_1_deg	15.346
r_scangle_it	5.159
r_scbond_it	3.189
r_mcangle_it	2.14
r_angle_refined_deg	1.9
r_mcbond_it	1.111
r_angle_other_deg	1.034
r_chiral_restr	0.133
r_bond_refined_d	0.021
r_bond_other_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3655
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	30

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data reduction
PHASER	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.