4F3W | pdb_00004f3w

Crystal structure of cytidine deaminase Cdd from Mycobacterium marinum

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	289	MymaA.00495.a.A1 PS00823 at 20 mg/mL against JCSG+ A8 0.2 M sodium formate, 20% PEG 3350, crystal tracking ID 232847a8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2	38.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.47	α = 100.19
b = 48.71	β = 110.42
c = 53.92	γ = 98.39

Symmetry
Space Group	P 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	RIGAKU SATURN 944+		2012-05-07	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	1.8	50	99.1	0.04	25.76	5	40341	39961		-3	24.135

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	1.8	1.85	96.1		0.181	5.98

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 3ijf	1.8	48.98	39960	1977	99.31	0.182	0.1801	0.1844	0.2181	0.2234	RANDOM	18.0363

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]
0.4	0.31	0.42	0.08	0.04	-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.73
r_dihedral_angle_4_deg	15.459
r_dihedral_angle_3_deg	13.433
r_dihedral_angle_1_deg	5.514
r_angle_refined_deg	1.478
r_angle_other_deg	0.941
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3437
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	4

Software

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