Experiment: 5YFC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	0.1 M Tris-HCl pH 8.5, 2.5 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.39	α = 90
b = 207.73	β = 90
c = 59.01	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2015-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.9793	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.76	59.01	98	0.066	0.071	0.027	0.994	22.6	7.2		134694

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	1.76	1.79	95.8		0.084	0.091	0.034	0.994		7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.76	59.01	128119	6535	97.99	0.1543	0.1521	0.1978	RANDOM	10.813

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]
-0.05		-0.04	-0.22		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.454
r_dihedral_angle_4_deg	18.792
r_dihedral_angle_3_deg	12.942
r_dihedral_angle_1_deg	5.86
r_angle_refined_deg	1.991
r_angle_other_deg	1.098
r_chiral_restr	0.136
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.454
r_dihedral_angle_4_deg	18.792
r_dihedral_angle_3_deg	12.942
r_dihedral_angle_1_deg	5.86
r_angle_refined_deg	1.991
r_angle_other_deg	1.098
r_chiral_restr	0.136
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10814
Nucleic Acid Atoms
Solvent Atoms	1462
Heterogen Atoms	101

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	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 R01GM133198.