Experiment: 5HGM

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	8.5	290	PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5), 10mM dATP

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.81	α = 90
b = 90.81	β = 90
c = 56.68	γ = 120

Symmetry
Space Group	P 6

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		2014-09-11	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 Merge I (Observed)	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	2.03	45.98	94.9	0.112	0.077	0.993	8.2	2.9		16259

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.08	69.1		0.551	0.418	0.42	1.9	2.4	877

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	2.04	45.98	15488	769	95.42	0.2373	0.2359	0.2632	RANDOM	26.365

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]
0.19	0.09		0.19		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.805
r_dihedral_angle_4_deg	13.086
r_dihedral_angle_3_deg	10.603
r_dihedral_angle_1_deg	4.762
r_mcangle_it	2.957
r_mcbond_it	1.763
r_mcbond_other	1.756
r_angle_refined_deg	0.991
r_angle_other_deg	0.864
r_chiral_restr	0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.805
r_dihedral_angle_4_deg	13.086
r_dihedral_angle_3_deg	10.603
r_dihedral_angle_1_deg	4.762
r_mcangle_it	2.957
r_mcbond_it	1.763
r_mcbond_other	1.756
r_angle_refined_deg	0.991
r_angle_other_deg	0.864
r_chiral_restr	0.05
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1551
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MAR345dtb	data collection
Aimless	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.