Experiment: 4EXQ

CRYSTAL STRUCTURE of UROPORPHYRINOGEN DECARBOXYLASE (UPD) FROM BURKHOLDERIA THAILANDENSIS E264

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.32	α = 90
b = 53.32	β = 90
c = 233.62	γ = 90

Symmetry
Space Group	P 41 21 2

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	ADSC QUANTUM 210		2012-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

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	50	99.6	0.061	16.26			41883		-3	25.07

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	1.65	1.69	99.9		0.521	2.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	50	41768	2105		0.179	0.178	0.1764	0.2	0.1992	RANDOM	19.86

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]
0.75			0.75		-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.257
r_dihedral_angle_4_deg	20.776
r_dihedral_angle_3_deg	12.643
r_dihedral_angle_1_deg	5.41
r_angle_refined_deg	1.315
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2678
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	1

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement