Experiment: 5GYC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		298	PEG 3350, 0.1 M tri-sodium acetate pH 4.5, 0.1 M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2	38.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.254	α = 90
b = 70.778	β = 90
c = 84.531	γ = 90

Symmetry
Space Group	P 2 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	ADSC QUANTUM 315		2015-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

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	1.4	50.01	96.8	0.033	16.9	3.8		49264

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45	93.7		0.423	0.845		3.6

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	5GV1	1.4	30	46647	2501	96.84	0.1729	0.1714	0.2032	RANDOM	19.294

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]
-0.85			-0.29		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.79
r_dihedral_angle_3_deg	13.241
r_dihedral_angle_4_deg	12.957
r_dihedral_angle_1_deg	7.113
r_mcangle_it	1.691
r_scbond_it	1.446
r_angle_refined_deg	1.436
r_mcbond_it	1.055
r_chiral_restr	0.092
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.79
r_dihedral_angle_3_deg	13.241
r_dihedral_angle_4_deg	12.957
r_dihedral_angle_1_deg	7.113
r_mcangle_it	1.691
r_scbond_it	1.446
r_angle_refined_deg	1.436
r_mcbond_it	1.055
r_chiral_restr	0.092
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms
Solvent Atoms	471
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 R01GM133198.