Experiment: 1YR8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	12% peg4000, 0.1M ammonium acetate, 0.1M tri-sodium citrate dihydrate, 20mM DTT, 10mM EDTA, 0.65mM GTP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.71	α = 90
b = 60.71	β = 90
c = 116.84	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 4	mirror	2004-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	20	98.5	0.075	0.075	20.76	11.6	10245	10088			48.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	98.2		0.4	0.4	7.03	12	696

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	1YR6	2.4	15	10203	9975	994	98.76	0.24201	0.24201	0.236	0.325	RANDOM	48.9

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]
3.63	1.82		3.63		-5.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.065
r_dihedral_angle_3_deg	19.379
r_dihedral_angle_4_deg	14.792
r_dihedral_angle_1_deg	5.844
r_scangle_it	1.698
r_mcangle_it	1.653
r_angle_refined_deg	1.192
r_scbond_it	1.123
r_mcbond_it	0.938
r_symmetry_hbond_refined	0.628

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.065
r_dihedral_angle_3_deg	19.379
r_dihedral_angle_4_deg	14.792
r_dihedral_angle_1_deg	5.844
r_scangle_it	1.698
r_mcangle_it	1.653
r_angle_refined_deg	1.192
r_scbond_it	1.123
r_mcbond_it	0.938
r_symmetry_hbond_refined	0.628
r_nbtor_refined	0.333
r_xyhbond_nbd_refined	0.31
r_nbd_refined	0.263
r_symmetry_vdw_refined	0.257
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1999
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
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.