Experiment: 1YYH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OT8	PDB ENTRY 1OT8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	ammonium hydrogen phosphate, sodium chloride, imidazole, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.84	α = 90
b = 96.84	β = 90
c = 108.996	γ = 120

Symmetry
Space Group	P 65

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		2005-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	1.9	83.92	98.5	0.079	0.079	12.4	3.6	44926	44926		2.5	26.9

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)
	1.9	1.94	98.6		0.385	0.385	12.4	3.6	3138

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 1OT8	1.901	83.92	44926	42631	2261	98.53	0.16272	0.16272	0.16112	0.19264	RANDOM	26.781

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]
0.72	0.36		0.72		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.899
r_dihedral_angle_4_deg	14.885
r_dihedral_angle_3_deg	12.908
r_scangle_it	5.779
r_dihedral_angle_1_deg	5.367
r_scbond_it	4.011
r_mcangle_it	3.487
r_mcbond_it	2.888
r_angle_refined_deg	1.425
r_nbtor_refined	0.295

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.899
r_dihedral_angle_4_deg	14.885
r_dihedral_angle_3_deg	12.908
r_scangle_it	5.779
r_dihedral_angle_1_deg	5.367
r_scbond_it	4.011
r_mcangle_it	3.487
r_mcbond_it	2.888
r_angle_refined_deg	1.425
r_nbtor_refined	0.295
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.195
r_symmetry_vdw_refined	0.12
r_chiral_restr	0.112
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2944
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.