Experiment: 1YDW

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10 MG/ML PROTEIN, 15% PEG4K, 0.168 M SODIUM CHLORIDE, 0.050 M PIPES, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.197	α = 90
b = 107.663	β = 90
c = 129.748	γ = 90

Symmetry
Space Group	P 21 21 21

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	BENT CYLINDRICAL SI-MIRROR (RH COATING)	2004-10-24	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	0.97927	APS	14-ID-B

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	2.488	33.749	98.3	0.107	13.245	13.4		29008

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)
	2.488	2.59	84.5		0.298	4.321	8.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.488	31.06	27390	1472	98.351	0.22155	0.21822	0.2261	0.28254	0.2865	RANDOM	33.072

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]
1.389			2.068		-3.457

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.318
r_dihedral_angle_4_deg	21.043
r_dihedral_angle_3_deg	19.93
r_dihedral_angle_1_deg	8.041
r_scangle_it	7.878
r_scbond_it	5.826
r_mcangle_it	3.216
r_angle_refined_deg	2.05
r_mcbond_it	1.757
r_symmetry_hbond_refined	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.318
r_dihedral_angle_4_deg	21.043
r_dihedral_angle_3_deg	19.93
r_dihedral_angle_1_deg	8.041
r_scangle_it	7.878
r_scbond_it	5.826
r_mcangle_it	3.216
r_angle_refined_deg	2.05
r_mcbond_it	1.757
r_symmetry_hbond_refined	0.34
r_nbtor_refined	0.326
r_nbd_refined	0.277
r_symmetry_vdw_refined	0.238
r_xyhbond_nbd_refined	0.216
r_chiral_restr	0.162
r_bond_refined_d	0.022
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5340
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	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.