Experiment: 2OYU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DIY	pdb entry 1diy (protein only)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	273	Sodium Citrate, Lithium Chloride, Sodium Azide, and beta-octylglucoside, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.41	α = 90
b = 181.41	β = 90
c = 103.398	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	100	CCD	MAR CCD 165 mm		2004-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	1.0	APS	32-ID

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	2.7	30	99.9	0.097	13	19	28072	28010		-3

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	2.7	2.76	100		0.335		15	1834

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1diy (protein only)	2.7	30	28072	27878	1400	99.55	0.241	0.241	0.292	RANDOM	51.256

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]
0.94	0.47		0.94		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.495
r_dihedral_angle_3_deg	20.021
r_dihedral_angle_4_deg	18.336
r_dihedral_angle_1_deg	6.412
r_scangle_it	1.665
r_angle_refined_deg	1.52
r_scbond_it	1.005
r_mcangle_it	0.656
r_mcbond_it	0.371
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.495
r_dihedral_angle_3_deg	20.021
r_dihedral_angle_4_deg	18.336
r_dihedral_angle_1_deg	6.412
r_scangle_it	1.665
r_angle_refined_deg	1.52
r_scbond_it	1.005
r_mcangle_it	0.656
r_mcbond_it	0.371
r_nbtor_refined	0.324
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.23
r_symmetry_hbond_refined	0.213
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4408
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	192

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOLREP	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 R01GM157729.