1R3W

Uroporphyrinogen Decarboxylase Y164F mutant in complex with coproporphyrinogen-III

X-RAY DIFFRACTION

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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
2.4	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.035	α = 90
b = 103.035	β = 90
c = 73.646	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	IMAGE PLATE	RIGAKU RAXIS IV		2003-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.7	87.71	99	0.071	0.071	12	5.9	49087	49087

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	1.7	1.76	99		0.39	0.39	1.8	5.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1URO	1.7	87.71	49087	47852	1226	98.66	0.1583	0.1583	0.15753	0.18887	RANDOM	23.551

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]
-1.01	-0.5		-1.01		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.09
r_scangle_it	4.288
r_scbond_it	2.597
r_mcangle_it	1.689
r_angle_refined_deg	1.549
r_mcbond_it	0.922
r_angle_other_deg	0.911
r_symmetry_vdw_other	0.328
r_nbd_other	0.244
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.211
r_symmetry_hbond_refined	0.151
r_chiral_restr	0.095
r_nbtor_other	0.083
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_gen_planes_other	0.01
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2797
Nucleic Acid Atoms
Solvent Atoms	354
Heterogen Atoms	48

Software

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