4GRD

Crystal structure of Phosphoribosylaminoimidazole carboxylase catalytic subunit from Burkholderia cenocepacia J2315

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XMP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	289	EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 0.1 M BICINE (PH 9.0), 10% (V/V) MPD. 20% ETHYLENE GLYCOL CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.51	α = 90
b = 117.18	β = 90
c = 122.31	γ = 90

Symmetry
Space Group	I 2 2 2

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 315		2012-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.977408	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	1.85		100	0.089	16.28			71473		-3	22.7

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	1.85	1.9	100		0.51	3.7

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	1XMP	1.85	48.122	71471	3618		0.148	0.147	0.176	RANDOM	12.97

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]
-0.29			-0.4		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.679
r_dihedral_angle_4_deg	21.028
r_dihedral_angle_3_deg	12.357
r_dihedral_angle_1_deg	5.6
r_angle_refined_deg	1.351
r_angle_other_deg	0.944
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4908
Nucleic Acid Atoms
Solvent Atoms	672
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement