4A8H

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A1S	PDB ENTRY 1A1S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		125 MM AMMONIUM SULPHATE, 17% PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.43 MM N-(PHOSPHONOACETYL)PUTRESCINE

Crystal Properties
Matthews coefficient	Solvent content
2.91	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.2	α = 90
b = 117.2	β = 90
c = 225.345	γ = 120

Symmetry
Space Group	P 63 2 2

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	ADSC QUANTUM 210r		2006-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16		ESRF	BM16

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	2.5	46	100	0.12	35.1	21.3		32509		2	36.5

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	2.5	20	100		0.43	9.5	21.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1A1S	2.5	29	30779	1637	100	0.184	0.18225	0.21651	RANDOM	19.296

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]
-0.19	-0.1		-0.19		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.861
r_dihedral_angle_4_deg	17.682
r_dihedral_angle_3_deg	13.016
r_dihedral_angle_1_deg	5.367
r_scangle_it	1.604
r_angle_refined_deg	1.165
r_scbond_it	1.013
r_angle_other_deg	0.874
r_mcangle_it	0.541
r_mcbond_it	0.271
r_chiral_restr	0.078
r_mcbond_other	0.063
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5380
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing