4A8P | pdb_00004a8p

Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N5-(phosphonoacetyl)-L-ornithine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A8H	PDB ENTRY 4A8H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		0.2 M AMMONIUM ACETATE, 25% POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS PH 5.5, 1 MM N5- (PHOSPHONOACETYL)-L-ORNITHINE

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.52	α = 105.43
b = 81.71	β = 102.8
c = 82.28	γ = 100.75

Symmetry
Space Group	P 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	MARRESEARCH		2009-12-13	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	30	87.5	0.12	10.9	1.6		114553		2	27.1

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	30	87.5		0.42	1.8	1.6

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 4A8H	2	25	108160	5763	87.57	0.198	0.19593	0.21	0.23732	0.25	RANDOM	33.299

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]
-0.59	-1.12	-0.94	-0.41	-1.11	-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.733
r_dihedral_angle_4_deg	16.611
r_dihedral_angle_3_deg	12.363
r_dihedral_angle_1_deg	4.762
r_scangle_it	1.321
r_angle_refined_deg	1.009
r_scbond_it	0.833
r_mcangle_it	0.423
r_mcbond_it	0.223
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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	15479
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	114

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing