4M0K

Crystal structure of adenine phosphoribosyltransferase from Rhodothermus marinus DSM 4252, NYSGRC Target 029775.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DY0	PDB ENTRY 2DY0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.2 M calcium chloride, 0.1 M HEPES:NAOH, pH 7.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.214	α = 87.3
b = 64.609	β = 77.23
c = 73.148	γ = 85.37

Symmetry
Space Group	P 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	CCD	RAYONIX MX225HE		2013-07-18		SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9791	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.4	50	95.9	0.07	12.7	3.8		135383

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	93		0.667		3.7	6539

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	PDB ENTRY 2DY0	1.4	20	135182	6751	95.89	0.185	0.1837	0.2095	RANDOM	22.5222

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]
1.17	-0.73	1.29	-0.88	-0.37	-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.536
r_dihedral_angle_3_deg	13.779
r_dihedral_angle_4_deg	13.105
r_dihedral_angle_1_deg	6.183
r_mcangle_it	2.091
r_scbond_it	1.768
r_angle_refined_deg	1.406
r_mcbond_it	1.183
r_chiral_restr	0.089
r_bond_refined_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.536
r_dihedral_angle_3_deg	13.779
r_dihedral_angle_4_deg	13.105
r_dihedral_angle_1_deg	6.183
r_mcangle_it	2.091
r_scbond_it	1.768
r_angle_refined_deg	1.406
r_mcbond_it	1.183
r_chiral_restr	0.089
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5383
Nucleic Acid Atoms
Solvent Atoms	602
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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.