2B69 | pdb_00002b69

Crystal Structure of Human UDP-glucoronic acid decarboxylase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	PEG3350, Zn (ac)2, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46	α = 90
b = 45	β = 97
c = 85	γ = 90

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD		2005-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97950	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.2	42.37	91.3				93023

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.26	58.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.21	40	84968	84968	4473	84.92	0.13559	0.13559	0.13418	0.139	0.16203	0.1361	RANDOM	12.954

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]
0.39		-0.07	0.22		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.702
r_dihedral_angle_4_deg	14.234
r_dihedral_angle_3_deg	11.353
r_sphericity_free	7.81
r_scangle_it	6.62
r_dihedral_angle_1_deg	5.668
r_scbond_it	5.245
r_sphericity_bonded	4.29
r_mcangle_it	3.951
r_mcbond_it	3.841
r_rigid_bond_restr	2.682
r_mcbond_other	2.356
r_angle_refined_deg	1.506
r_angle_other_deg	0.877
r_symmetry_vdw_refined	0.3
r_symmetry_hbond_refined	0.284
r_nbd_refined	0.214
r_symmetry_vdw_other	0.21
r_nbd_other	0.172
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.086
r_nbtor_other	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2439
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing