3O7H | pdb_00003o7h

Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q37	PDB ENTRY 2Q37

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	22-26% PEG-8000, 0.25 M sodium acetate in pH 6.5 cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.799	α = 113.18
b = 49.338	β = 116.49
c = 51.687	γ = 94.26

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	ADSC QUANTUM 210		2010-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.987	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.79	50	93.8	0.03	27.8	1.7	33900	31800		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.79	1.82	75		0.142	4.7	1.5

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 2Q37	1.79	23.13	30202	1603	93	0.22226	0.22104	0.2183	0.24474	0.244	RANDOM	20.076

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]
0.06	0.05	0.04	-0.01	0.05	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.943
r_dihedral_angle_4_deg	16.681
r_dihedral_angle_3_deg	13.25
r_dihedral_angle_1_deg	3.804
r_scangle_it	1.54
r_angle_refined_deg	0.894
r_scbond_it	0.866
r_mcangle_it	0.582
r_mcbond_it	0.295
r_chiral_restr	0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.943
r_dihedral_angle_4_deg	16.681
r_dihedral_angle_3_deg	13.25
r_dihedral_angle_1_deg	3.804
r_scangle_it	1.54
r_angle_refined_deg	0.894
r_scbond_it	0.866
r_mcangle_it	0.582
r_mcbond_it	0.295
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2527
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.