1VK3 | pdb_00001vk3

Crystal structure of Phosphoribosylformylglycinamidine synthase II (TM1246) from Thermotoga maritima at 2.15 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	293	30.00% PEG 200, 0.10M Tris pH 8.0, 7% NP_PEG 4000 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	41.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.775	α = 90
b = 72.689	β = 90
c = 128.418	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		2003-12-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0035, 0.9796	ALS	8.2.1

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	2.15	72.69	90.8	0.089	10.2	3.2		28272			38.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.15	2.21	56.8		0.554	1.3	1.9	1292

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.15	63.26	26869	1368	90.59	0.18974	0.18645	0.19	0.25423	0.26	RANDOM	24.896

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]
-0.14			-1.52		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.563
r_dihedral_angle_4_deg	17.362
r_dihedral_angle_3_deg	16.934
r_scangle_it	7.269
r_dihedral_angle_1_deg	6.044
r_scbond_it	5.423
r_mcangle_it	2.597
r_mcbond_it	1.758
r_angle_refined_deg	1.315
r_symmetry_vdw_refined	0.204

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.563
r_dihedral_angle_4_deg	17.362
r_dihedral_angle_3_deg	16.934
r_scangle_it	7.269
r_dihedral_angle_1_deg	6.044
r_scbond_it	5.423
r_mcangle_it	2.597
r_mcbond_it	1.758
r_angle_refined_deg	1.315
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.194
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4444
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	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.