4WIG | pdb_00004wig

Crystal structure of E47D mutant cytidine deaminase from Mycobacterium tuberculosis (MtCDA E47D)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M HEPES pH7.5; 4.3 M Sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66	α = 90
b = 76.98	β = 90
c = 112.84	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	MARMOSAIC 225 mm CCD		2014-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.459	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.758	112.84	98.6	0.108	0.113	0.033	13.4	11.4	28875	28875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.758	1.85	90.8		0.528	0.528	0.167	1.4	10.8	3826

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.758	22.02	28844	1465	99.6	0.2124	0.2114	0.22	0.2293	0.23	RANDOM	14.533

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]
-0.01			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.828
r_dihedral_angle_3_deg	14.123
r_dihedral_angle_4_deg	12.022
r_dihedral_angle_1_deg	5.448
r_angle_refined_deg	1.196
r_angle_other_deg	0.751
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.828
r_dihedral_angle_3_deg	14.123
r_dihedral_angle_4_deg	12.022
r_dihedral_angle_1_deg	5.448
r_angle_refined_deg	1.196
r_angle_other_deg	0.751
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1832
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.