Experiment: 6YHH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NOW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	14% PEGMME 5K, 0.1 M Na-Malonate

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.986	α = 90
b = 124.547	β = 90
c = 151.587	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	120	PIXEL	DECTRIS PILATUS3 S 6M		2016-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

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	1.7	49	99.9	0.077	0.084	0.032	0.999	17.2	6.5		158136

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	1.7	1.73	98.4		0.44	0.496	0.223	0.868		4.7

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	1NOW	1.7	49	150222	7814	99.87	0.1443	0.1427	0.175	RANDOM	15.113

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]
1.35			-1.11		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.452
r_dihedral_angle_4_deg	21.429
r_dihedral_angle_3_deg	11.555
r_dihedral_angle_1_deg	6.3
r_angle_refined_deg	1.945
r_angle_other_deg	0.952
r_chiral_restr	0.136
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.452
r_dihedral_angle_4_deg	21.429
r_dihedral_angle_3_deg	11.555
r_dihedral_angle_1_deg	6.3
r_angle_refined_deg	1.945
r_angle_other_deg	0.952
r_chiral_restr	0.136
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10208
Nucleic Acid Atoms
Solvent Atoms	1544
Heterogen Atoms	22

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Auto-Rickshaw	phasing

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.