1VQT

Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EIX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	277	12.0% PEG-20000, 0.1M MES pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.688	α = 90
b = 85.55	β = 130.2
c = 48.725	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	ADSC		2004-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	99	99.47	0.066	28.05	4.81		17410			55.68

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	1.9	1.93	95.32		1.34	3.41	836

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	1EIX	2	27	14180	758	99.61	0.18343	0.18139	0.22088	RANDOM	58.589

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]
2.07		-1.36	-3.3		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.102
r_dihedral_angle_4_deg	19.956
r_dihedral_angle_3_deg	14.754
r_dihedral_angle_1_deg	6.244
r_scangle_it	3.323
r_scbond_it	2.256
r_angle_refined_deg	1.671
r_mcangle_it	1.476
r_mcbond_it	0.995
r_angle_other_deg	0.839
r_symmetry_vdw_refined	0.494
r_mcbond_other	0.257
r_symmetry_hbond_refined	0.233
r_nbd_refined	0.213
r_nbtor_refined	0.185
r_nbd_other	0.183
r_symmetry_vdw_other	0.178
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.103
r_nbtor_other	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1457
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	36

Software

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