Experiment: 6RYG

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RYM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	2.5 M ammonium sulfate, 0.1 M tris

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.17	α = 90
b = 50.17	β = 90
c = 52.247	γ = 90

Symmetry
Space Group	P 43

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 315		2007-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.92	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	0.974	50.17	81.2	0.05	0.05	0.059	22.9	7.7		61295

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)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.97	1.02	20.5		0.216	0.216	0.315	3.2	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6RYM	0.974	50	58175	3086	81.13	0.1349	0.1347	0.14	0.1388	0.15	RANDOM	14.148

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]
-0.25			-0.25		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.741
r_dihedral_angle_4_deg	13.245
r_dihedral_angle_3_deg	11.609
r_rigid_bond_restr	7.733
r_dihedral_angle_1_deg	6.37
r_angle_refined_deg	1.654
r_angle_other_deg	1.568
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.741
r_dihedral_angle_4_deg	13.245
r_dihedral_angle_3_deg	11.609
r_rigid_bond_restr	7.733
r_dihedral_angle_1_deg	6.37
r_angle_refined_deg	1.654
r_angle_other_deg	1.568
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	896
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	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.