1R3Y | pdb_00001r3y

Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-III

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	6.5	294	PBG, PBG-D and U3S were added to the protein solution in an anaerobic chamber. URO-D was active under these conditions, converting uro'gen-III to cop'gen-III. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.14	α = 90
b = 103.14	β = 90
c = 74.56	γ = 120

Symmetry
Space Group	P 31 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	ADSC QUANTUM 4		2001-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.1000	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	87.71	100	0.091	0.091	11	5.5	45954	45954

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	100		0.423	0.423	2.8	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	1URO	1.755	87.71	45954	44553	1378	99.71	0.15905	0.15905	0.1582	0.17	0.18574	0.2	RANDOM	24.457

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]
-1.09	-0.55		-1.09		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.062
r_scangle_it	4.989
r_scbond_it	2.994
r_mcangle_it	1.963
r_angle_refined_deg	1.627
r_mcbond_it	1.059
r_angle_other_deg	0.896
r_symmetry_vdw_other	0.352
r_nbd_other	0.242
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.218
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.175
r_chiral_restr	0.098
r_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2798
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	48

Software

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