3MW8

Crystal structure of an UROPORPHYRINOGEN-III SYNTHASE (Sama_3255) from SHEWANELLA AMAZONENSIS SB2B at 1.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1500M di-ammonium hydrogen phosphate, 33.0000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.39	α = 90
b = 50.073	β = 90.04
c = 58.255	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

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	1.65	38.525	99.2	0.048	13.48			35551		-3	25.002

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)
	1.65	1.71	99.8		0.442	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.65	38.525	35537	1814	99.26	0.177	0.175	0.203	RANDOM	29.321

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]
0.26		-1.48	-0.86		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.784
r_dihedral_angle_4_deg	22.58
r_dihedral_angle_3_deg	13.025
r_scangle_it	7.541
r_dihedral_angle_1_deg	6.002
r_scbond_it	5.099
r_mcangle_it	3.063
r_mcbond_it	2.013
r_angle_refined_deg	1.576
r_angle_other_deg	0.977

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.784
r_dihedral_angle_4_deg	22.58
r_dihedral_angle_3_deg	13.025
r_scangle_it	7.541
r_dihedral_angle_1_deg	6.002
r_scbond_it	5.099
r_mcangle_it	3.063
r_mcbond_it	2.013
r_angle_refined_deg	1.576
r_angle_other_deg	0.977
r_mcbond_other	0.596
r_chiral_restr	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1770
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.