Experiment: 1YAB

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	293	18% MPD, 100mM MES buffer, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.7	70

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.173	α = 90
b = 100.173	β = 90
c = 87.853	γ = 120

Symmetry
Space Group	P 31 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		2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.979277	ALS	5.0.2

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	3.4	87.7	95.9	0.07	7.3	11	7246	7246

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	3.4	3.52	93.4		0.289	1.8	11	996

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	1O6A.pdb	3.4	19.9	7246	6906	340	99.04	0.22735	0.22735	0.22437	0.28624	RANDOM	112.247

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]
6.52	3.26		6.52		-9.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.642
r_dihedral_angle_3_deg	23.97
r_dihedral_angle_4_deg	17.903
r_dihedral_angle_1_deg	8.738
r_scangle_it	3.353
r_angle_refined_deg	1.76
r_scbond_it	1.708
r_mcangle_it	1.396
r_mcbond_it	0.746
r_nbtor_refined	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.642
r_dihedral_angle_3_deg	23.97
r_dihedral_angle_4_deg	17.903
r_dihedral_angle_1_deg	8.738
r_scangle_it	3.353
r_angle_refined_deg	1.76
r_scbond_it	1.708
r_mcangle_it	1.396
r_mcbond_it	0.746
r_nbtor_refined	0.326
r_nbd_refined	0.264
r_symmetry_vdw_refined	0.261
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.119
r_bond_refined_d	0.014
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1352
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.