Experiment: 5VZN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2MBW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris-Hcl, 1 mM EDTA, pH 7.4 2.56 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.8	α = 90
b = 29.26	β = 105.79
c = 63.949	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV++		2013-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.7	26.42	80.5	0.03	0.038	0.023	0.999	30.1	2.4		11177

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	80		0.099	0.131	0.083	0.983		2.2

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	2MBW	1.7	26.42	10618	558	80.26	0.1395	0.1368	0.1903	RANDOM	15.596

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]
-0.63			1.05		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.65
r_dihedral_angle_4_deg	13.41
r_dihedral_angle_3_deg	12.1
r_dihedral_angle_1_deg	5.561
r_angle_refined_deg	1.999
r_angle_other_deg	1.099
r_chiral_restr	0.144
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_gen_planes_other	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.65
r_dihedral_angle_4_deg	13.41
r_dihedral_angle_3_deg	12.1
r_dihedral_angle_1_deg	5.561
r_angle_refined_deg	1.999
r_angle_other_deg	1.099
r_chiral_restr	0.144
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_gen_planes_other	0.007
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1203
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	59

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.