Experiment: 3RYD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.15M Sodium Potassium tartrate, 22%(w/v) PEG 3350, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.878	α = 90
b = 68.046	β = 90
c = 143.898	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	93	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2011-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.367	71.949	99.2	0.132	13.6	7	20973	20973

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.49	95.9		0.621	0.621	0.674	0.257	1.2	6.7	2911

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.37	19.68	20921	1070	99.19	0.1945	0.1899	0.2784	RANDOM	28.8

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]
1.34			-2.37		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.247
r_dihedral_angle_4_deg	20.783
r_dihedral_angle_3_deg	19.523
r_dihedral_angle_1_deg	7.349
r_scangle_it	3.246
r_scbond_it	2.096
r_angle_refined_deg	1.663
r_mcangle_it	1.245
r_mcbond_it	0.674
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.247
r_dihedral_angle_4_deg	20.783
r_dihedral_angle_3_deg	19.523
r_dihedral_angle_1_deg	7.349
r_scangle_it	3.246
r_scbond_it	2.096
r_angle_refined_deg	1.663
r_mcangle_it	1.245
r_mcbond_it	0.674
r_chiral_restr	0.115
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4098
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	36

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

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.