Experiment: 4AXS

Structure of Carbamate Kinase from Mycoplasma penetrans

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E19	PDB ENTRY 1E19

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.8	α = 90
b = 51.8	β = 90
c = 174.162	γ = 120

Symmetry
Space Group	P 32 2 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 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.38	44.86	97.7	0.07	11.8	4.8		11222		2	45.29

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	2.38	2.51	92.2		0.39	2.5	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1E19	2.5	44.86	1.35	9818	465	98.17	0.2332	0.2306	0.2291	0.2872	0.2842

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]
11.9406			11.9406		-23.8811

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	20.881
f_angle_d	1.109
f_chiral_restr	0.077
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2155
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	10

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing