Experiment: 1YJ5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	293	0.1M Tris (pH 8.3 - 8.7), 18-20% PEG 5000 MME, 0.1M Li2SO4, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.8	31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.473	α = 90
b = 169.872	β = 90
c = 77.016	γ = 90

Symmetry
Space Group	P 21 21 2

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	ADSC QUANTUM 315		2003-09-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0199, 0.9793, 0.9797	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	30	99	0.095	13.1			31529	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	91.2		0.448	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	THROUGHOUT	2.8	29.75	31529	29868	1562	99.54	0.22029	0.21856	0.2525	RANDOM	26.374

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]
-2.19			5.27		-3.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.012
r_dihedral_angle_3_deg	16.24
r_dihedral_angle_4_deg	15.69
r_dihedral_angle_1_deg	4.818
r_angle_refined_deg	0.923
r_scangle_it	0.772
r_scbond_it	0.478
r_mcangle_it	0.361
r_nbtor_refined	0.305
r_mcbond_it	0.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.012
r_dihedral_angle_3_deg	16.24
r_dihedral_angle_4_deg	15.69
r_dihedral_angle_1_deg	4.818
r_angle_refined_deg	0.923
r_scangle_it	0.772
r_scbond_it	0.478
r_mcangle_it	0.361
r_nbtor_refined	0.305
r_mcbond_it	0.201
r_xyhbond_nbd_refined	0.146
r_nbd_refined	0.143
r_symmetry_hbond_refined	0.095
r_symmetry_vdw_refined	0.089
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6706
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.