1R3S | pdb_00001r3s

Uroporphyrinogen Decarboxylase single mutant D86G in complex with coproporphyrinogen-I

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.947	α = 90
b = 102.947	β = 90
c = 72.585	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	1.65	87.71	97	0.072	0.072	10	5	51831	51831

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	1.65	1.71	80		0.236	0.236	1.8	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	PDB ENTRY 1URO	1.65	87.71	51831	50541	1290	96.64	0.16321	0.16321	0.16255	0.17	0.19	0.2	RANDOM	23.05

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]
-1.53	-0.76		-1.53		2.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.584
r_scangle_it	4.311
r_scbond_it	2.602
r_angle_refined_deg	1.845
r_mcangle_it	1.734
r_mcbond_it	0.944
r_angle_other_deg	0.891
r_symmetry_vdw_refined	0.396
r_symmetry_vdw_other	0.357
r_nbd_other	0.244
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.21
r_symmetry_hbond_refined	0.181
r_chiral_restr	0.094
r_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_other	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2794
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	48

Software

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