Experiment: 4YQE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.1 M MES/Imidazol, 12.5 % PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.2M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.179	α = 90
b = 61.179	β = 90
c = 169.992	γ = 90

Symmetry
Space Group	P 41 21 2

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		2014-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.33	42.5	99.9	0.049	18.02	5.63	142025	141939			20.75

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	1.33	1.41	99.8		0.657	2.36

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	2RG1	1.33	42.5	71491	3763	99.92	0.1266	0.1248	0.1608	RANDOM	21.479

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.375
r_sphericity_free	28.296
r_dihedral_angle_4_deg	12.897
r_sphericity_bonded	11.336
r_dihedral_angle_3_deg	10.971
r_dihedral_angle_1_deg	5.576
r_rigid_bond_restr	3.235
r_mcangle_it	2.998
r_mcbond_it	2.511
r_mcbond_other	2.502

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.375
r_sphericity_free	28.296
r_dihedral_angle_4_deg	12.897
r_sphericity_bonded	11.336
r_dihedral_angle_3_deg	10.971
r_dihedral_angle_1_deg	5.576
r_rigid_bond_restr	3.235
r_mcangle_it	2.998
r_mcbond_it	2.511
r_mcbond_other	2.502
r_angle_refined_deg	1.642
r_angle_other_deg	1.117
r_chiral_restr	0.094
r_gen_planes_refined	0.015
r_bond_refined_d	0.013
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2806
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building
XSCALE	data scaling

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.