2C8C | pdb_00002c8c

Structure of the ARTT motif Q212A mutant C3bot1 Exoenzyme (NAD-bound state, crystal form I)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				22.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V

Crystal Properties
Matthews coefficient	Solvent content
2.57	51.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.048	α = 90
b = 76.135	β = 102.74
c = 120.432	γ = 90

Symmetry
Space Group	C 1 2 1

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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.7	39.84	95.8	0.09	12.4	4		24821		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 1GZF	2.7	39.84	23555	1262	100	0.243	0.241	0.21	0.283	0.25	RANDOM	56.76

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]
3.59		-0.74	4.06		-7.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.582
r_scangle_it	3.444
r_scbond_it	2.007
r_mcangle_it	1.711
r_angle_refined_deg	1.609
r_angle_other_deg	1.291
r_mcbond_it	0.91
r_nbd_other	0.242
r_nbd_refined	0.229
r_symmetry_vdw_other	0.208
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.171
r_symmetry_vdw_refined	0.147
r_chiral_restr	0.118
r_nbtor_other	0.084
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6422
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	159

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing