Experiment: 1YI7

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.1 M HEPES, 0.2 M AMMONIUM SULFATE, 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.13	α = 90
b = 143.73	β = 90
c = 188.69	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	105	IMAGE PLATE	RIGAKU RAXIS IV	VARIMAX	2004-12-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.9	40	100	0.11	10.8	7.8	190582	190582		-5	17.8

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	1.9	1.97	100		0.38	4.8	7.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1Y7B	1.9	20	184667	184667	5740	100	0.144	0.144	0.142	0.202	RANDOM	24.975

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]
0.4			-0.02		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.893
r_dihedral_angle_4_deg	19.428
r_scangle_it	13.932
r_scbond_it	13.324
r_dihedral_angle_3_deg	13.265
r_mcangle_it	7.155
r_dihedral_angle_1_deg	6.745
r_mcbond_it	6.061
r_angle_refined_deg	1.379
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.893
r_dihedral_angle_4_deg	19.428
r_scangle_it	13.932
r_scbond_it	13.324
r_dihedral_angle_3_deg	13.265
r_mcangle_it	7.155
r_dihedral_angle_1_deg	6.745
r_mcbond_it	6.061
r_angle_refined_deg	1.379
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.121
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17364
Nucleic Acid Atoms
Solvent Atoms	2586
Heterogen Atoms	219

Software

Software
Software Name	Purpose
REFMAC	refinement
AMoRE	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.