3CNN | pdb_00003cnn

GTP-bound structure of TM YlqF

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	297	100mM HEPES (pH 7.5), 5% (v/v) isopropanol, 20% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.264	α = 90
b = 75.295	β = 90
c = 105.106	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	100	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1	1.23985	PAL/PLS	6C1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	20				12903	12903

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PUJ	2.3	19.06	12844	1263	98.65	0.235	0.229	0.2253	0.283	0.2782	RANDOM	50.081

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]
2.25			2.13		-4.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.479
r_dihedral_angle_3_deg	17.801
r_dihedral_angle_4_deg	17.336
r_dihedral_angle_1_deg	6.558
r_scangle_it	2.691
r_scbond_it	1.596
r_mcangle_it	1.391
r_angle_refined_deg	1.373
r_mcbond_it	0.791
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.197
r_symmetry_vdw_refined	0.189
r_chiral_restr	0.111
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1824
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction