Experiment: 5YX1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CVD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	8.5	293	35% PEG 6000, 5 mM DTT, 2 mM MgCl2, 2 mM Glutathione, 2% Dioxane, 50 mM Tris-HCl, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.447	α = 92.2
b = 47.119	β = 98.67
c = 91.924	γ = 90

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS3 6M		2016-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	1.39	70	89.3	0.096	6.7	3.1		144547

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	1.39	1.4	86.5		0.57		2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2CVD	1.39	47.94	123473	6537	80.42	0.1863	0.1847	0.2159	RANDOM	20.617

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]
-0.02	0.05	0.03	-0.16	0.04	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.21
r_dihedral_angle_4_deg	13.73
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	5.359
r_angle_refined_deg	1.566
r_angle_other_deg	0.801
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.21
r_dihedral_angle_4_deg	13.73
r_dihedral_angle_3_deg	12.42
r_dihedral_angle_1_deg	5.359
r_angle_refined_deg	1.566
r_angle_other_deg	0.801
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6552
Nucleic Acid Atoms
Solvent Atoms	895
Heterogen Atoms	187

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.