Experiment: 3KNU

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	289	21.0 mg/mL protein, expression tag not cleaved prior to crystallization; 0.1 M Na citrate pH 4.0, 8% PEG 3350, 10% glycerol, crystal tracking ID 205756f1 and q1x5b1-7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.291	α = 90
b = 104.304	β = 90
c = 99.105	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 315		2009-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	2.25	50	100	0.064	30.95	7.2		52092

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	2.25	2.33	99.9		0.584	3.4	6.9	5115

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	3IEF	2.25	50	51937	2645	99.66	0.205	0.203	0.234	RANDOM	25.526

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]
0.65			0.22		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.335
r_dihedral_angle_4_deg	15.763
r_dihedral_angle_3_deg	14.533
r_dihedral_angle_1_deg	5.091
r_scangle_it	3.484
r_scbond_it	2.174
r_mcangle_it	1.541
r_angle_refined_deg	1.295
r_mcbond_it	0.83
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.335
r_dihedral_angle_4_deg	15.763
r_dihedral_angle_3_deg	14.533
r_dihedral_angle_1_deg	5.091
r_scangle_it	3.484
r_scbond_it	2.174
r_mcangle_it	1.541
r_angle_refined_deg	1.295
r_mcbond_it	0.83
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6003
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

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.