Experiment: 5CXY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	293	130 mM (NH)4H2PO4, 22% PEG2000 and 50 mM PIPES pH 7.3

Crystal Properties
Matthews coefficient	Solvent content
2.9	61.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.84	α = 90
b = 96.64	β = 90
c = 124.78	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR scanner 345 mm plate		2015-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002	1.502

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	52.72	100	0.084	0.047	0.997	11.8	4.1		48673

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.22	100		0.604	0.34	0.709	2.3	4.1	4142

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	5BO6	2.15	52.72	46200	2407	99.97	0.2	0.1981	0.2352	RANDOM	38.139

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]
1.58			-0.07		-1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.725
r_dihedral_angle_4_deg	17.329
r_dihedral_angle_3_deg	16.441
r_dihedral_angle_1_deg	6.303
r_mcangle_it	5.133
r_mcbond_it	3.481
r_mcbond_other	3.472
r_angle_refined_deg	1.89
r_angle_other_deg	1.474
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.725
r_dihedral_angle_4_deg	17.329
r_dihedral_angle_3_deg	16.441
r_dihedral_angle_1_deg	6.303
r_mcangle_it	5.133
r_mcbond_it	3.481
r_mcbond_other	3.472
r_angle_refined_deg	1.89
r_angle_other_deg	1.474
r_chiral_restr	0.107
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4805
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	289

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	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.