Experiment: 6GD8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LYC	5LYC chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	24 % PEG 3350 0.27 M NaCl 0.09 M MES pH 5.5 (2x protein solution : 1x crystallisation condition)

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.68	α = 90
b = 66.68	β = 90
c = 142.881	γ = 120

Symmetry
Space Group	P 31

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 EIGER X 9M		2017-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.5	71.44	99.7	0.131	0.158	0.086	0.984	5.7	3.1		24569

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	99.9		0.39	0.47	0.259	0.607		3.1

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	5LYC chain A	2.5	57.75	23441	1090	99.75	0.1772	0.1761	0.1998	RANDOM	41.858

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]
13.98			13.98		-27.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.034
r_dihedral_angle_4_deg	21.613
r_dihedral_angle_3_deg	12.728
r_dihedral_angle_1_deg	6.04
r_angle_refined_deg	1.375
r_angle_other_deg	0.903
r_chiral_restr	0.09
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.034
r_dihedral_angle_4_deg	21.613
r_dihedral_angle_3_deg	12.728
r_dihedral_angle_1_deg	6.04
r_angle_refined_deg	1.375
r_angle_other_deg	0.903
r_chiral_restr	0.09
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3384
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	497

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
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.