Experiment: 3VAZ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K73	PDB ENTRY 3K73

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	22% PEG 400, 0.2M CaCl2, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.389	α = 90
b = 155.389	β = 90
c = 317.849	γ = 120

Symmetry
Space Group	P 62 2 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	IMAGE PLATE	RIGAKU RAXIS IV++		2011-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	3.19	29.742	99.6	0.315	13.8			38297		-3	17.228

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.19	3.39	99		0.733	0.751	5.35

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	PDB ENTRY 3K73	3.19	29.74	38297	1915	100	0.2059	0.2022	0.19	0.277	0.26	RANDOM	19.828

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]
-1.77	-0.88		-1.77		2.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.934
r_dihedral_angle_4_deg	19.342
r_dihedral_angle_3_deg	15.637
r_dihedral_angle_1_deg	5.018
r_angle_refined_deg	0.995
r_mcangle_it	0.291
r_mcbond_it	0.163
r_scangle_it	0.122
r_chiral_restr	0.064
r_scbond_it	0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.934
r_dihedral_angle_4_deg	19.342
r_dihedral_angle_3_deg	15.637
r_dihedral_angle_1_deg	5.018
r_angle_refined_deg	0.995
r_mcangle_it	0.291
r_mcbond_it	0.163
r_scangle_it	0.122
r_chiral_restr	0.064
r_scbond_it	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14999
Nucleic Acid Atoms
Solvent Atoms	414
Heterogen Atoms	308

Software

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