3BGE | pdb_00003bge

Crystal structure of the C-terminal fragment of AAA+ATPase from Haemophilus influenzae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R9G	PDB entry 2R9G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.1M tri-Sodium citrate pH 5.6, 2M Ammonium sulfate, 0.2M Potassium sodium tartrate tetrahydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.085	α = 90
b = 93.085	β = 90
c = 83.413	γ = 90

Symmetry
Space Group	I 4

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	MAR CCD 165 mm		2007-08-20	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-08-16	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID
2	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

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	1.85	23.12	99.4	0.079	4.8	3.1	30371	30371

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.85	1.93	100		0.44	0.38	2.2	3.1	7540

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	SAD	THROUGHOUT	PDB entry 2R9G	1.85	23.12	29276	29276	1468	96.41	0.189	0.189	0.187	0.19	0.24	0.24	RANDOM	24.288

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]
-0.54			-0.54		1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.249
r_dihedral_angle_4_deg	17.124
r_dihedral_angle_3_deg	15.639
r_scangle_it	6.62
r_dihedral_angle_1_deg	5.309
r_scbond_it	4.597
r_mcangle_it	2.696
r_mcbond_it	1.835
r_angle_refined_deg	1.349
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.249
r_dihedral_angle_4_deg	17.124
r_dihedral_angle_3_deg	15.639
r_scangle_it	6.62
r_dihedral_angle_1_deg	5.309
r_scbond_it	4.597
r_mcangle_it	2.696
r_mcbond_it	1.835
r_angle_refined_deg	1.349
r_nbtor_refined	0.321
r_nbd_refined	0.235
r_symmetry_hbond_refined	0.225
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.199
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2578
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
PHASER	phasing

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.