3OB6 | pdb_00003ob6

Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	24-28% PEG400, 2mM Cymal-5, 1mM LDAO, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.071	α = 90
b = 77.204	β = 106.79
c = 104.451	γ = 90

Symmetry
Space Group	P 1 21 1

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 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9791	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	30	93.3	6.8	3.3	25006	24681	1.5	1.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3	3.11	73.4		2.4	2.6

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 (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 3LRB	3	25	23349	23349	1255	92.96	0.24473	0.24328	0.25	0.27202	0.28	RANDOM	47.695

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]
-7.01		-1.97	7.67		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.67
r_dihedral_angle_3_deg	20.656
r_dihedral_angle_4_deg	16.245
r_dihedral_angle_1_deg	6.665
r_scangle_it	1.694
r_angle_refined_deg	1.418
r_angle_other_deg	1.063
r_scbond_it	1.024
r_mcangle_it	0.745
r_mcbond_it	0.381
r_chiral_restr	0.094
r_mcbond_other	0.07
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6411
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	24

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DNA	data collection
DENZO	data reduction
SCALEPACK	data scaling