Experiment: 5IDJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IDM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	30% PEG 550 MME, 30% PEG 2000 MME, Morpheus buffer 1 pH 6.5 and Morpheus carboxylic acids

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.856	α = 90
b = 164.856	β = 90
c = 48.001	γ = 120

Symmetry
Space Group	P 63 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	PIXEL	DECTRIS PILATUS 6M		2015-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9999	SLS	X06DA

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	3.01	142.598	91.4	0.103	15	11.3		7413			76.14

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	3.01	3.17	51.2		0.327	2.2	1.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	5IDM	3.02	47.59	1.35	7403	392	92.51	0.2416	0.239	0.22	0.2886	0.28	RANDOM	71.4027

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.62
r_dihedral_angle_3_deg	21.562
r_dihedral_angle_4_deg	21.299
r_dihedral_angle_1_deg	7.677
r_mcangle_it	4.719
r_mcbond_other	3.02
r_mcbond_it	3.019
r_angle_refined_deg	1.645
r_angle_other_deg	1.025
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.62
r_dihedral_angle_3_deg	21.562
r_dihedral_angle_4_deg	21.299
r_dihedral_angle_1_deg	7.677
r_mcangle_it	4.719
r_mcbond_other	3.02
r_mcbond_it	3.019
r_angle_refined_deg	1.645
r_angle_other_deg	1.025
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1869
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	28

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
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.