Experiment: 5D0R

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CLK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.1 M SODIUM ACETATE PH 4.8, 0.2 M TRI-SODIUM-CITRATE, 15% (W/V) PEG 4000, 10% (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.403	α = 90
b = 99.403	β = 90
c = 99.978	γ = 120

Symmetry
Space Group	P 63

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	COLLIMATOR	2014-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

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	2.24	86.23	100	0.0138	11.9	5.1		27051

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	2.24	2.37	99		0.0894	1.7	5.1

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	4CLK	2.24	86.23	25668	1383	99.74	0.1806	0.1773	0.2437	RANDOM	35.966

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]
-0.22	-0.11		-0.22		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.296
r_dihedral_angle_3_deg	16.216
r_dihedral_angle_4_deg	15.617
r_dihedral_angle_1_deg	7.642
r_mcangle_it	3.946
r_mcbond_it	2.402
r_mcbond_other	2.397
r_angle_refined_deg	2.177
r_angle_other_deg	1.134
r_chiral_restr	0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.296
r_dihedral_angle_3_deg	16.216
r_dihedral_angle_4_deg	15.617
r_dihedral_angle_1_deg	7.642
r_mcangle_it	3.946
r_mcbond_it	2.402
r_mcbond_other	2.397
r_angle_refined_deg	2.177
r_angle_other_deg	1.134
r_chiral_restr	0.131
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3654
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	71

Software

Software
Software Name	Purpose
MOSFLM	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

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.