Experiment: 5D8U

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1 M HEPES sodium, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.881	α = 90
b = 89.881	β = 90
c = 134.148	γ = 90

Symmetry
Space Group	I 4 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	CCD	RAYONIX MX300-HS		2014-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97921	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.29	50	99.6	0.062	0.064	0.018	10.8	12.4		12715

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	2.29	2.37	95.9		0.819	0.864	0.267	0.792		9.6	1219

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	PDB entry 5CZN	2.29	46	12091	622	99.55	0.2003	0.1982	0.2408	RANDOM	65.79

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]
1.06			1.06		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.759
r_dihedral_angle_3_deg	17.981
r_dihedral_angle_4_deg	16.89
r_dihedral_angle_1_deg	7.901
r_mcangle_it	4.83
r_mcbond_it	3.199
r_mcbond_other	3.183
r_angle_refined_deg	2.371
r_angle_other_deg	1.246
r_chiral_restr	0.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.759
r_dihedral_angle_3_deg	17.981
r_dihedral_angle_4_deg	16.89
r_dihedral_angle_1_deg	7.901
r_mcangle_it	4.83
r_mcbond_it	3.199
r_mcbond_other	3.183
r_angle_refined_deg	2.371
r_angle_other_deg	1.246
r_chiral_restr	0.133
r_bond_refined_d	0.026
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1403
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	24

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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.