3DMO | pdb_00003dmo

1.6 A crystal structure of cytidine deaminase from Burkholderia pseudomallei

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	289	35% MPD, 0.1M Na/K PHOSPHATE, pH 6.2, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.495	α = 90
b = 72.308	β = 111.29
c = 83.327	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS	2008-04-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.00	APS	23-ID-D

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	1.6	50	99.8	0.091	6.4	3.7		88018

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)
	1.6	1.66	100		0.779		3.7	8725

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	34.54	87989	4417	99.75	0.2	0.199	0.2004	0.224	0.225	RANDOM	24.804

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]
0.12		-0.02	-0.09		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.339
r_dihedral_angle_3_deg	14.072
r_dihedral_angle_4_deg	13.117
r_dihedral_angle_1_deg	4.818
r_scangle_it	2.494
r_scbond_it	1.48
r_angle_refined_deg	1.152
r_mcangle_it	0.897
r_mcbond_it	0.526
r_nbtor_refined	0.298
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.133
r_symmetry_vdw_refined	0.114
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3854
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	41

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction