2D30 | pdb_00002d30

Crystal Structure of Cytidine Deaminase Cdd-2 (BA4525) from Bacillus Anthracis at 2.40A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	PEG2000 MME, Ca_acetate, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.792	α = 90
b = 50.552	β = 132.1
c = 70.438	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 QUANTUM 4	Rh coated Si mirror	2004-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87000	SRS	PX9.6

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	2.4	50	92.7	0.074	15.5	3.5	9578	9578

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	62.1		0.172	5.7	2.5	630

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	MOLECULAR REPLACEMENT	THROUGHOUT	1JTK	2.4	27.89	9117	9117	458	100	0.16825	0.16825	0.16429	0.17	0.25075	0.26	RANDOM	30.112

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]
-0.63		1.05	-0.02		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.25
r_dihedral_angle_3_deg	19.541
r_dihedral_angle_4_deg	15.845
r_scangle_it	6.865
r_dihedral_angle_1_deg	5.821
r_scbond_it	5.075
r_mcangle_it	2.822
r_mcbond_it	2.091
r_angle_refined_deg	1.693
r_angle_other_deg	0.93
r_symmetry_hbond_refined	0.269
r_mcbond_other	0.257
r_nbd_refined	0.2
r_symmetry_vdw_other	0.2
r_xyhbond_nbd_refined	0.195
r_nbd_other	0.194
r_nbtor_refined	0.172
r_symmetry_vdw_refined	0.172
r_chiral_restr	0.099
r_nbtor_other	0.087
r_bond_refined_d	0.019
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1880
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing