3SEC

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	Trisodium Citrate, Dioxane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.244	α = 90
b = 103.574	β = 90
c = 73.739	γ = 90

Symmetry
Space Group	C 2 2 21

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 315		2006-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

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	1.7	50	99.9	0.084	11.7	9.6		24704

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	1.7	1.73	99.7		0.489	4.43	7.4

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	1DV7	1.7	50	24027	648	99.66	0.15661	0.15584	0.18683	RANDOM	17.911

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]
0.4			-0.75		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.238
r_dihedral_angle_4_deg	18.547
r_dihedral_angle_3_deg	15.164
r_dihedral_angle_1_deg	5.687
r_scangle_it	3.857
r_scbond_it	2.508
r_angle_refined_deg	1.564
r_mcangle_it	1.476
r_mcbond_it	0.963
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.238
r_dihedral_angle_4_deg	18.547
r_dihedral_angle_3_deg	15.164
r_dihedral_angle_1_deg	5.687
r_scangle_it	3.857
r_scbond_it	2.508
r_angle_refined_deg	1.564
r_mcangle_it	1.476
r_mcbond_it	0.963
r_nbtor_refined	0.313
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.103
r_symmetry_hbond_refined	0.1
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1622
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	28

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.