Experiment: 4YSH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RYI	PDB 1RYI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	298	0.1 M phosphate-citrate buffer, 7% 2-propanol, 0.4 M LiSO4

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.945	α = 90
b = 87.945	β = 90
c = 413.456	γ = 120

Symmetry
Space Group	P 65 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	95	CCD	ADSC QUANTUM 270		2014-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

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	2.2	50	98.6	0.096	0.098	0.022	11.5	20.6		48899			34.4

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	2.2	2.28	99.7		0.417	0.426	0.089	0.972	10.5	22.2	4774

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 1RYI	2.2	50	46153	2463	98.34	0.2345	0.2328	0.2661	RANDOM	44.542

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]
0.66	0.33		0.66		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.05
r_dihedral_angle_4_deg	19.13
r_dihedral_angle_3_deg	18.227
r_dihedral_angle_1_deg	5.804
r_scangle_it	1.885
r_angle_refined_deg	1.344
r_scbond_it	1.099
r_mcangle_it	0.804
r_mcbond_it	0.429
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.05
r_dihedral_angle_4_deg	19.13
r_dihedral_angle_3_deg	18.227
r_dihedral_angle_1_deg	5.804
r_scangle_it	1.885
r_angle_refined_deg	1.344
r_scbond_it	1.099
r_mcangle_it	0.804
r_mcbond_it	0.429
r_chiral_restr	0.101
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5510
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	136

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
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.