Experiment: 6YDK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	PEG 4000 (24% w/v), sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), beta-phosphoglucomutase (0.5 mM). Seeded with 10,000x dilution of much smaller protein crystals grown under the same conditions but with 0.2 mM beta-phosphoglucomutase.

Crystal Properties
Matthews coefficient	Solvent content
9.62	87.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.3	α = 90
b = 56.24	β = 90
c = 77.66	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M-F		2018-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	2.02	43.95	98.8	0.075	0.081	0.031	0.999	14.4	6.6		15683			32.196

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	2.02	2.05	88.9		0.953	1.09	0.506	0.556	1.2	3.7

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	2WHE	2.02	43.95	14863	777	98.49	0.2174	0.2156	0.2507	RANDOM	42.707

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]
-0.27			-0.36		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.886
r_dihedral_angle_4_deg	22.923
r_dihedral_angle_3_deg	15.025
r_dihedral_angle_1_deg	6.164
r_angle_refined_deg	1.489
r_angle_other_deg	0.958
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.886
r_dihedral_angle_4_deg	22.923
r_dihedral_angle_3_deg	15.025
r_dihedral_angle_1_deg	6.164
r_angle_refined_deg	1.489
r_angle_other_deg	0.958
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1706
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XDS	data reduction
xia2	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.