Experiment: 5HGK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H4E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	290	PEG3350 (20%), Ammonium chloride (0.2M, pH 6.3)

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.72	α = 90
b = 23.85	β = 96.31
c = 129.549	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2012-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.763	128.765	91.9	0.065	0.074	0.033	13.3	4.6	25066	25066

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.763	1.86	80.6		0.227	0.227	0.115	3.2	4.6	3188

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	3H4E	1.763	128.76	23827	1229	92.4	0.1916	0.1899	0.2241	RANDOM	28.533

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]
0.1		1	-0.79		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_4_deg	16.35
r_dihedral_angle_3_deg	13.564
r_dihedral_angle_1_deg	5.134
r_mcangle_it	3.454
r_mcbond_it	2.524
r_mcbond_other	2.506
r_angle_refined_deg	1.222
r_angle_other_deg	1.122
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.391
r_dihedral_angle_4_deg	16.35
r_dihedral_angle_3_deg	13.564
r_dihedral_angle_1_deg	5.134
r_mcangle_it	3.454
r_mcbond_it	2.524
r_mcbond_other	2.506
r_angle_refined_deg	1.222
r_angle_other_deg	1.122
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2233
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MAR345dtb	data collection
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction

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.