1R3V | pdb_00001r3v

Uroporphyrinogen Decarboxylase single mutant D86E 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

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
2.4	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.111	α = 90
b = 103.111	β = 90
c = 73.313	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 IIC		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	1.9	20	98	0.134	0.134	9	6.2	35021	35021

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	1.9	1.97	95		0.399	0.399	2.5	6.2

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	1.9	19.5	35021	33590	1403	100	0.15203	0.15203	0.15052	0.17	0.1869	0.19	RANDOM	16.723

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]
-0.56	-0.28		-0.56		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.515
r_scangle_it	4.745
r_scbond_it	2.873
r_mcangle_it	1.769
r_angle_refined_deg	1.63
r_mcbond_it	0.994
r_angle_other_deg	0.933
r_symmetry_vdw_other	0.351
r_nbd_other	0.25
r_nbd_refined	0.227
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.208
r_symmetry_vdw_refined	0.186
r_chiral_restr	0.108
r_nbtor_other	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
r_bond_other_d	0.002
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	2803
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	52

Software

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