3R5H | pdb_00003r5h

Crystal Structure of ADP-AIR 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	3Q20	PDB ENTRY 3Q20

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M MES, 5mM DTT, 11% glycerol, 10% PEG 6000, Hampton Research Addition Screen Condition 46, 10mM MgCl2; Crystal soaked for one minute with 10mM AIR, pH 6.5, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.442	α = 90
b = 82.785	β = 90
c = 168.233	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		2011-02-16	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	2.2	20	98.8	0.054	22.57		41312	41312		-3	35.399

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.33	94.9		0.199	0.218	8.65

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 3Q20	2.2	19.76	41257	41257	2089	99.36	0.1821	0.1821	0.1787	0.18	0.2484	0.24	RANDOM	29.1989

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	40.906
r_dihedral_angle_3_deg	14.663
r_dihedral_angle_4_deg	13.713
r_dihedral_angle_1_deg	5.844
r_scangle_it	3.183
r_scbond_it	1.844
r_mcangle_it	1.353
r_angle_refined_deg	1.314
r_mcbond_it	0.721
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.906
r_dihedral_angle_3_deg	14.663
r_dihedral_angle_4_deg	13.713
r_dihedral_angle_1_deg	5.844
r_scangle_it	3.183
r_scbond_it	1.844
r_mcangle_it	1.353
r_angle_refined_deg	1.314
r_mcbond_it	0.721
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5925
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms	94

Software

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

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.