3QFF

Crystal Structure of ADP complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q2O	PDB entry 3Q2O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M MES, 5mM DTT, 9% glycerol, 10% PEG6000, Hampton Research Silver Bullet Bio additive C3/27 and 3mM ADP, pH 6.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.421	α = 90
b = 82.089	β = 90
c = 166.768	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	MARMOSAIC 300 mm CCD		2010-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.00	APS	22-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	1.96		97.1	0.091	14.43			55699		-3	39.42

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	1.96	2.08	82.1		0.816	1.98

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 3Q2O	1.96	19.97	55669	2832	97.16	0.2015	0.1989	0.2515	RANDOM	34.6697

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.811
r_dihedral_angle_3_deg	14.506
r_dihedral_angle_4_deg	9.74
r_dihedral_angle_1_deg	5.538
r_scangle_it	3.03
r_scbond_it	1.765
r_mcangle_it	1.259
r_angle_refined_deg	1.182
r_mcbond_it	0.669
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.811
r_dihedral_angle_3_deg	14.506
r_dihedral_angle_4_deg	9.74
r_dihedral_angle_1_deg	5.538
r_scangle_it	3.03
r_scbond_it	1.765
r_mcangle_it	1.259
r_angle_refined_deg	1.182
r_mcbond_it	0.669
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5876
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	54

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.