Experiment: 1TM5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TM3	PDB entry 1tm3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	sodium citrate, isopropanol, PEG monomethyl ether 750, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.781	α = 90
b = 93.781	β = 90
c = 185.758	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	ADSC QUANTUM 4		2002-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.0	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.45	81.65	95.6	0.043	9.7	2.3	81746	81746	-3	-3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1tm3	1.45	81.65	-3	-3	81746	77651	4095	95.62	0.16173	0.16173	0.16082	0.17892	inherited from 1tm3	16.825

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]
0.28	0.14		0.28		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.769
r_scangle_it	4.549
r_scbond_it	2.775
r_angle_refined_deg	1.88
r_mcangle_it	1.642
r_mcbond_it	0.974
r_symmetry_vdw_refined	0.416
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.769
r_scangle_it	4.549
r_scbond_it	2.775
r_angle_refined_deg	1.88
r_mcangle_it	1.642
r_mcbond_it	0.974
r_symmetry_vdw_refined	0.416
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.122
r_metal_ion_refined	0.064
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2549
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
TRUNCATE	data scaling
EPMR	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.