Experiment: 5GYA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5	298	PEG 6000, 0.1 M NaOAc, 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.501	α = 79.57
b = 46.25	β = 83.1
c = 78.204	γ = 66.25

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	CCD	Nonius Kappa CCD		2014-12-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.54

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	1.93	30	93.9	0.033	23.9	2.9		37834

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	1.93	2	83.2		0.101		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	THROUGHOUT	5GV1	1.93	30	35939	1895	94.32	0.1684	0.1659	0.1662	0.2176	0.2174	RANDOM	14.73

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]
-0.42	0.53	-0.46	0.62	0.01	-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.906
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	13.685
r_dihedral_angle_1_deg	7.14
r_mcangle_it	1.467
r_angle_refined_deg	1.375
r_scbond_it	0.998
r_mcbond_it	0.85
r_chiral_restr	0.098
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.906
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	13.685
r_dihedral_angle_1_deg	7.14
r_mcangle_it	1.467
r_angle_refined_deg	1.375
r_scbond_it	0.998
r_mcbond_it	0.85
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4310
Nucleic Acid Atoms
Solvent Atoms	679
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data collection
HKL-2000	data scaling
PHASER	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.