2PN1 | pdb_00002pn1

Crystal structure of carbamoylphosphate synthase large subunit (split gene in MJ) (ZP_00538348.1) from Exiguobacterium sp. 255-15 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.7	277	NANODROP, 24.0% PEG 8000, 0.25M Sodium chloride, 0.1M Phosphate-citrate pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.6	α = 90
b = 61.21	β = 124.02
c = 76.88	γ = 90

Symmetry
Space Group	C 1 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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-04-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97920	SSRL	BL9-2

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	27.587	91.2	0.063	7.47			23426			33.272

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	2.07	83.5		0.351	2.6		3879

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 (All)	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	MAD	THROUGHOUT	2	27.587	23425	1200	97.7	0.195	0.195	0.192	0.2	0.239	0.24	RANDOM	28.712

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]
0.49		-0.84	-0.55		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.793
r_dihedral_angle_3_deg	10.878
r_dihedral_angle_4_deg	10.831
r_scangle_it	6.094
r_scbond_it	4.548
r_dihedral_angle_1_deg	3.951
r_mcangle_it	2.351
r_angle_refined_deg	1.622
r_mcbond_it	1.562
r_angle_other_deg	1.306
r_mcbond_other	0.368
r_nbd_refined	0.168
r_symmetry_vdw_other	0.162
r_nbtor_refined	0.152
r_nbd_other	0.14
r_symmetry_vdw_refined	0.121
r_xyhbond_nbd_refined	0.099
r_chiral_restr	0.091
r_symmetry_hbond_refined	0.086
r_nbtor_other	0.072
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2390
Nucleic Acid Atoms
Solvent Atoms	165
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing