2C8A | pdb_00002c8a

Structure of the wild-type C3bot1 Exoenzyme (Nicotinamide-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
2.26	45.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.741	α = 90
b = 74.638	β = 101.04
c = 118.962	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 BM30A		ESRF	BM30A

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	1.69	24.32	99.5	0.04	25.6	4		99953		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	1.7	24.33	94351	4950	100	0.207	0.205	0.21	0.235	0.24	RANDOM	25.96

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]
-0.84		-0.43	2.1		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.071
r_scangle_it	2.365
r_scbond_it	1.371
r_mcangle_it	1.025
r_angle_refined_deg	0.946
r_angle_other_deg	0.699
r_mcbond_it	0.531
r_nbd_other	0.231
r_nbd_refined	0.184
r_symmetry_vdw_other	0.173
r_xyhbond_nbd_refined	0.131
r_symmetry_vdw_refined	0.121
r_symmetry_hbond_refined	0.116
r_nbtor_other	0.08
r_chiral_restr	0.058
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	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	6430
Nucleic Acid Atoms
Solvent Atoms	782
Heterogen Atoms	56

Software

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