3MPZ

Crystal structure of CYTIDINE DEAMINASE from Mycobacterium smegmatis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IJF	pdb entry 3ijf

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	MD PACT SCREEN E9; 20% PEG 3350, 200MM NA/K TARTRATE; protein at 40MG/ML, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.28	α = 90
b = 96.11	β = 90
c = 178.19	γ = 90

Symmetry
Space Group	C 2 2 21

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	RIGAKU SATURN 944+		2010-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.7	50	98.2	0.043	22.01	4	51708	50775		-3	20.35

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	1.7	1.74	85.1		0.271	3.2	1.9	3219

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3ijf	1.7	50	51708	50615	2570	97.9	0.158	0.158	0.156	0.192	RANDOM	11.7

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]
-0.05			0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.512
r_dihedral_angle_4_deg	16.442
r_dihedral_angle_3_deg	14.112
r_dihedral_angle_1_deg	5.178
r_scangle_it	3.612
r_scbond_it	2.255
r_mcangle_it	1.558
r_angle_refined_deg	1.436
r_angle_other_deg	1.047
r_mcbond_it	0.884
r_mcbond_other	0.219
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	3520
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	4

Software

Software
Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling