4E4T | pdb_00004e4t

Crystal structure of Phosphoribosylaminoimidazole carboxylase, ATPase subunit from Burkholderia ambifaria

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	BuamA.00036.a.A1 PS01234 at 46 mg/mL against Wiz3/4 condition H5, 20% PEG 8000, 0.1 M Hepes pH 7.5, 0.2 M ammonium sulfate, 10% isopropanol with 20% ethylene glycol as cryo-protectant, crystal tracking ID 228074h5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.43	α = 90
b = 73.39	β = 90
c = 159.29	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 315r		2011-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	1.55	50	99.6	0.054	15.76	4.5	111915	111431		-3	24.671

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	1.55	1.59	99.4		0.473	2.74

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	3q2o	1.55	50	111430	5586	99.56	0.1785	0.1772	0.18	0.2028	0.21	RANDOM	22.5074

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]
-0.96			0.09		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.498
r_dihedral_angle_4_deg	13.067
r_dihedral_angle_3_deg	10.752
r_dihedral_angle_1_deg	5.45
r_angle_refined_deg	1.427
r_angle_other_deg	1.11
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.498
r_dihedral_angle_4_deg	13.067
r_dihedral_angle_3_deg	10.752
r_dihedral_angle_1_deg	5.45
r_angle_refined_deg	1.427
r_angle_other_deg	1.11
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5612
Nucleic Acid Atoms
Solvent Atoms	801
Heterogen Atoms	25

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.