2HCB | pdb_00002hcb

Structure of AMPPCP-bound DnaA from Aquifex aeolicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L8Q	PDB ENTRY 1L8Q RESIDUES 77 TO 240

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	292	50mM Na cacodylate, 125mM KCl, 125mM Kbr, 5% Glycerol, 25% 1,2-Propanediol, 5% PEG MME2K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.076	α = 90
b = 117.714	β = 90
c = 200.994	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		CCD	ADSC QUANTUM 210		2005-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.51	40.38		0.175	6.6	3.6		25439		2

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	PDB ENTRY 1L8Q RESIDUES 77 TO 240	3.51	30	24077	1293	84.56	0.26738	0.26572	0.25	0.29796	0.25	RANDOM	94.374

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]
-6.72			12.85		-6.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.615
r_dihedral_angle_3_deg	19.348
r_dihedral_angle_4_deg	15.755
r_mcangle_it	11.575
r_mcbond_it	8.768
r_dihedral_angle_1_deg	6.367
r_scangle_it	4.06
r_scbond_it	3.175
r_angle_refined_deg	1.001
r_nbtor_refined	0.322
r_nbd_refined	0.269
r_symmetry_vdw_refined	0.257
r_xyhbond_nbd_refined	0.186
r_symmetry_hbond_refined	0.171
r_metal_ion_refined	0.127
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10437
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data scaling
PHASER	phasing