4CZC

Crystal structure of the siroheme decarboxylase NirDL in co-complex with iron-uroporphyrin III analogue

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				FOR THE CRYSTALLIZATION OF THE NIRDL-FE-URO III CO-COMPLEX, NIRDL (7 MG/ML) WAS INCUBATED 30 MIN ON ICE WITH 0.5 MM FE-URO III (DISSOLVED IN 50 % DMSO) PRIOR TO CRYSTAL SETUP. PROTEIN-FE-URO III WAS MIXED WITH EQUAL AMOUNTS OF PRECIPITANT SOLUTION (27 % (V/V) MPD, 0.1 M MES, PH 5.5, AND 9.95 MM SPERMIDINE). CRYSTALS WERE CRYO-PROTECTED WITH 25-33 % (V/V) GLYCEROL OR ADDITIONAL 33 % (V/V) MPD PRIOR TO FLASH FREEZING IN LIQUID NITROGEN.

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.75	α = 90
b = 72.6	β = 102.06
c = 51.11	γ = 90

Symmetry
Space Group	C 1 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	RIGAKU SATURN 944PLUS		2012-09-26	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.9	28.7	97.8	0.04	22.7	3.1		8137		2.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	92.6		0.44	2.57	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4CH7	2.9	28.68	7730	407	97.78	0.23215	0.22939	0.28432	RANDOM	51.182

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]
0.25		-4.75	2.43		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.713
r_dihedral_angle_3_deg	15.678
r_dihedral_angle_4_deg	13.711
r_dihedral_angle_1_deg	6.338
r_mcangle_it	6.167
r_scbond_it	4.368
r_mcbond_it	3.693
r_mcbond_other	3.685
r_angle_refined_deg	1.657
r_angle_other_deg	0.769
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2507
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing