3R8C | pdb_00003r8c

Crystal structure of cytidylate kinase (Cmk) from Mycobacterium abscessus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H92	pdb entry 2h92

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	protein at 27.9 mg/mL 12.5% PEG 1000, 12.5% PEG 2250, 12.5% MPD, 0.1 M MOPS/NaHepes, 30 mM MgCl2, 30 mM CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.13	α = 90
b = 70.49	β = 91.95
c = 92.32	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	RIGAKU SATURN 944+	VariMax	2011-02-23	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	2.2	50	94.6	0.054	15.76	3.2	22360	21148		-3	29.545

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	2.2	2.26	90.9		0.201	6.45	3.1	1673

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 2h92	2.2	50	21127	1056	94.49	0.2162	0.2143	0.2289	0.2538	0.2372	RANDOM	27.7739

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]
1.37		-1.29	-2.68		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.231
r_dihedral_angle_4_deg	20.698
r_dihedral_angle_3_deg	14.434
r_dihedral_angle_1_deg	5.197
r_scangle_it	3.346
r_scbond_it	2.094
r_angle_refined_deg	1.457
r_mcangle_it	1.214
r_mcbond_it	0.678
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2871
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms

Software

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